Longtable with multicolumn and parbox spacing issues

• There is no need for \parbox, column type p is better regarding the vertical spacing. The width is calculated from the three column width of the default p columns. Each column get two \tabcolsep, therefore 4\tabcolsep are added for the two suppressed columns.

  \newlength\mymulticolwidth
  \setlength{\mymulticolwidth}{\dimexpr 2.5cm + 3.5cm + 2.5cm + 4\tabcolsep\relax}
  

• The example also adds \extrarowheight of package array that is added at the top of the rows.

• The enumerations can be set by environment enumerate with some adaptations of Donald Arsenau that defines a new column type and is shown in Danie Els' answer. I have only set \leftmargini to get rid of the large indentation. If the numbers exceed 9, then the code needs some refinement.

Example file:

\documentclass{article}
\usepackage[
  hmargin=15mm,
  vmargin=15mm,
]{geometry}
\usepackage{longtable}
\usepackage{array}

\setlength{\extrarowheight}{2pt}
\newlength\mymulticolwidth

\makeatletter
\newcolumntype{e}[1]{%--- Enumerated cells ---
   >{\minipage[t]{\linewidth}%
     \NoHyper% Hyperref adds a vertical space because of anchor whatsit.
     \let\\\tabularnewline
     \settowidth{\leftmargini}{9.\hspace{\labelsep}}%
     \enumerate
        \addtolength{\rightskip}{0pt plus 50pt}% for raggedright
        \setlength{\itemsep}{-\parsep}}%
   p{#1}%
   <{\@finalstrut\@arstrutbox\endenumerate
     \endNoHyper
     \endminipage}}

\AtBeginDocument{%
    \@ifpackageloaded{hyperref}{}%
        {\let\NoHyper\relax\let\endNoHyper\relax}}
\makeatother

\begin{document}
\setlength{\mymulticolwidth}{\dimexpr 2.5cm + 3.5cm + 2.5cm + 4\tabcolsep\relax}
\newcommand{\mymulticol}[1]{%
  \multicolumn{3}{p{\mymulticolwidth}|}{#1}%
}
\begin{longtable}{| p{3.5cm} | p{2.5cm} | p{3.5cm} | p{2.5cm} |}
\caption{Use case detail}\label{chap3:tab1}\\
\multicolumn{4}{c}{}\\
\endfirsthead
\multicolumn{4}{c}{\tablename\ \thetable\ -- \textit{Continued from previous page}}\\
\multicolumn{4}{c}{}\\
\hline
\endhead
\hline \multicolumn{4}{r}{\tablename\ \thetable\ -- \textit{Continued on next page}} \\
\endfoot
\hline  
\endlastfoot
%
\hline
% --------------------------------------------------------------------------------------------------------------
Use Case ID: & \multicolumn{3}{l|}{1}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Use Case Name: & \multicolumn{3}{l|}{FIXME - Section Name}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Created by: & & Date created: &\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Actors & \multicolumn{3}{l|}{Doctor}\\
& \multicolumn{3}{l|}{Patient}\\
& \multicolumn{3}{l|}{Patients' Database}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Description: & \mymulticol{%
  The doctor logs into the system, creates/updates the patient medical record, prints the informed consent form and collects it after the patient has signed it.}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Preconditions: & \multicolumn{3}{e{\mymulticolwidth}|}{%
  \item The doctor is logged into the web software.
  \item There is no record for the patient on the patients' database.}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Postconditions: & \multicolumn{3}{l|}{ }\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Trigger: & \mymulticol{%
  The doctor logs in the system and presses the \textit{Login} button}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Normal flow: & \multicolumn{3}{e{\mymulticolwidth}|}{%
  \item the doctor clicks on the \textit{Patients} icon;
  \item the doctor clicks on the \textit{Add} button;   
  \item the doctor prints the consent form by clicking on the dedicated button;
  \item the doctor fills in the patient's details;
  \item the doctor collects the signed patient's consent form and ticks the dedicated check box;
  \item the doctor saves the patient's record by clicking the \textit{Save} button.}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Alternative flows: & \multicolumn{3}{l|}{ }\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Exceptions: & \multicolumn{3}{l|}{ }\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Notes and issues: & \multicolumn{3}{l|}{ }\\
% --------------------------------------------------------------------------------------------------------------
\hline
\end{longtable}
\end{document} 

The principle can be extended, example for package enumerate:

\documentclass{article}
\usepackage[
  hmargin=15mm,
  vmargin=15mm,
]{geometry}
\usepackage{longtable}
\usepackage{array}
\usepackage{enumerate}

\setlength{\extrarowheight}{2pt}
\newlength\mymulticolwidth

\makeatletter
\newcolumntype{e}[1]{%--- Enumerated cells ---
   >{\minipage[t]{\linewidth}%
     \NoHyper% Hyperref adds a vertical space because of anchor whatsit.
     \let\\\tabularnewline
     \settowidth{\leftmargini}{9.\hspace{\labelsep}}%
     \enumerate
        \addtolength{\rightskip}{0pt plus 50pt}% for raggedright
        \setlength{\itemsep}{-\parsep}}%
   p{#1}%
   <{\@finalstrut\@arstrutbox\endenumerate
     \endNoHyper
     \endminipage}}

\newcolumntype{E}[2]{%--- Enumerated cells ---
   >{\minipage[t]{\linewidth}%
     \NoHyper% Hyperref adds a vertical space because of anchor whatsit.
     \let\\\tabularnewline
     \settowidth{\leftmargini}{9a.\hspace{\labelsep}}%
     \enumerate[{#2}]%
        \addtolength{\rightskip}{0pt plus 50pt}% for raggedright
        \setlength{\itemsep}{-\parsep}}%
   p{#1}%
   <{\@finalstrut\@arstrutbox\endenumerate
     \endNoHyper
     \endminipage}}

\AtBeginDocument{%
    \@ifpackageloaded{hyperref}{}%
        {\let\NoHyper\relax\let\endNoHyper\relax}}
\makeatother

\begin{document}
\setlength{\mymulticolwidth}{\dimexpr 2.5cm + 3.5cm + 2.5cm + 4\tabcolsep\relax}
\newcommand{\mymulticol}[1]{%
  \multicolumn{3}{p{\mymulticolwidth}|}{#1}%
}
\begin{longtable}{| p{3.5cm} | p{2.5cm} | p{3.5cm} | p{2.5cm} |}
\caption{Use case detail}\label{chap3:tab1}\\
\multicolumn{4}{c}{}\\
\endfirsthead
\multicolumn{4}{c}{\tablename\ \thetable\ -- \textit{Continued from previous page}}\\
\multicolumn{4}{c}{}\\
\hline
\endhead
\hline \multicolumn{4}{r}{\tablename\ \thetable\ -- \textit{Continued on next page}} \\
\endfoot
\hline  
\endlastfoot
%
\hline
% --------------------------------------------------------------------------------------------------------------
Use Case ID: & \multicolumn{3}{l|}{1}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Use Case Name: & \multicolumn{3}{l|}{FIXME - Section Name}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Created by: & & Date created: &\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Actors & \multicolumn{3}{l|}{Doctor}\\
& \multicolumn{3}{l|}{Patient}\\
& \multicolumn{3}{l|}{Patients' Database}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Description: & \mymulticol{%
  The doctor logs into the system, creates/updates the patient medical record, prints the informed consent form and collects it after the patient has signed it.}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Preconditions: & \multicolumn{3}{e{\mymulticolwidth}|}{%
  \item The doctor is logged into the web software.
  \item There is no record for the patient on the patients' database.}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Postconditions: & \multicolumn{3}{l|}{ }\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Trigger: & \mymulticol{%
  The doctor logs in the system and presses the \textit{Login} button}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Normal flow: & \multicolumn{3}{e{\mymulticolwidth}|}{%
  \item the doctor clicks on the \textit{Patients} icon;
  \item the doctor clicks on the \textit{Add} button;   
  \item the doctor prints the consent form by clicking on the dedicated button;
  \item the doctor fills in the patient's details;
  \item the doctor collects the signed patient's consent form and ticks the dedicated check box;
  \item the doctor saves the patient's record by clicking the \textit{Save} button.}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Alternative flows: & \multicolumn{3}{E{\mymulticolwidth}{1{a}.}|}{%
  \item lorem ipsum
  \item lorem ipsum
  \item lorem ipsum}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Exceptions: & \multicolumn{3}{l|}{ }\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Notes and issues: & \multicolumn{3}{l|}{ }\\
% --------------------------------------------------------------------------------------------------------------
\hline
\end{longtable}
\end{document} 

I think you had too many columns and too much markup generally, I think I 'd do this unless you really need the lists to break over a page.

\documentclass{article}
\usepackage{longtable,array}
\setlength\extrarowheight{3pt}

\begin{document}

\begin{longtable}{| p{3.5cm} | p{9cm} |}
\caption{Use case detail}\label{chap3:tab1}\\[12pt]
\endfirsthead
\multicolumn{2}{c}{\tablename\ \thetable\ -- \textit{Continued from previous page}}\\[12pt]
\hline
\endhead
\hline
\multicolumn{2}{r}{\tablename\ \thetable\ -- \textit{Continued on next page}} \\
\endfoot
\hline
\endlastfoot

\hline
% --------------------------------------------------------------------------------------------------------------
Use Case ID: & 1\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Use Case Name: & FIXME - Section Name\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Created by:&\hspace{2cm}\vrule\ Date created:\hspace{2cm}\vrule\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Actors &
Doctor\newline
Patient\newline
Patients' Database\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Description: &
The doctor logs into the system, creates/updates the patient medical record, prints the informed consent form and collects it after the patient has signed it.\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Preconditions: &\mbox{}\par\vspace{-\baselineskip}
\begin{enumerate}
\item The doctor is logged into the web software.
\item There is no record for the patient on the patients' database.
\end{enumerate}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Postconditions: & \\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Trigger: & The doctor logs in the system and presses the \textit{Login} button\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Normal flow: &\mbox{}\par\vspace{-\baselineskip}
\begin{enumerate}
\item the doctor clicks on the \textit{Patients} icon;
\item the doctor clicks on the \textit{Add} button;
\item the doctor prints the consent form by clicking on the dedicated button;
\item the doctor fills in the patient's details;
\item the doctor collects the signed patient's consent form and ticks the dedicated check box;
\end{enumerate}\\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Alternative flows: & \\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Exceptions: & \\
% --------------------------------------------------------------------------------------------------------------
\hline
% --------------------------------------------------------------------------------------------------------------
Notes and issues: &\\
% --------------------------------------------------------------------------------------------------------------
\hline
\end{longtable}

\end{document}