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A 'quick and dirty' solution, with \newlistof command from tocloft package.

\documentclass{article}%

\usepackage{blindtext}
\usepackage[titles]{tocloft}

\usepackage{etoolbox}


\newcounter{example}[section]
\renewcommand{\theexample}{\arabic{section}.\arabic{example}}%
\newenvironment{example}[1][]{%
  \refstepcounter{example}%  
  \ifblank{#1}{%
    }{%
      \addcontentsline{exp}{examples}{\protect\numberline{\theexample}#1}%
    }%
  \par\medskip%
  \noindent\textbf{Example~\theexample. #1} \rmfamily}{\medskip}%




\newcommand{\listexampletitle}{List of Examples}

\newlistof[section]{examples}{exp}{\listexampletitle}%

\cftsetindents{examples}{1.5em}{3.0em}%
%\cftpagenumbersoff{examples}
\setlength{\cftexamplesnumwidth}{1.5cm}


\begin{document}

\section{Introduction}%

\listofexamples


\begin{example}[title]

This is the first example. The counter will be reset at each section.
\end{example}


\begin{example}
This is the 2nd  example, but has no entry to the toc!
\end{example}


\section{A section}
\blindtext[1]
\begin{example}[Another title]
\blindtext[2] 

Another example.
\end{example}


\begin{example}[Yet Another title]
\blindtext[3]% 

Yet Another example.
\end{example}

\end{document}

Another version without section numbers for examples

Disclaimer I do not recommend dropping the section number for examples, as it will lead to more difficult identification which example is meant, especially if examples have the same title (due to some reason)

\documentclass{article}%

\usepackage{blindtext}
\usepackage[titles]{tocloft}

\usepackage{etoolbox}


\newcounter{example}
\renewcommand{\theexample}{\arabic{example}}% To be on the safe side!
\newenvironment{example}[1][]{%
  \refstepcounter{example}%  
  \ifblank{#1}{%
    }{%
      \addcontentsline{exp}{examples}{\protect\numberline{\theexample}#1}%
    }%
  \par\medskip%
  \noindent\textbf{Example~\theexample. #1} \rmfamily}{\medskip}%




\newcommand{\listexampletitle}{List of Examples}

\newlistof[section]{examples}{exp}{\listexampletitle}%

\cftsetindents{examples}{1.5em}{3em}% Some indentation -- change to 0pt if needed
%\cftpagenumbersoff{examples}
\setlength{\cftexamplesnumwidth}{1.5cm}%


\begin{document}

\section{Introduction}%

\listofexamples


\begin{example}[title]

This is the first example. The counter will be reset at each section.
\end{example}


\begin{example}
This is the 2nd  example, but has no entry to the toc!
\end{example}


\section{A section}
\blindtext[1]
\begin{example}[Another title]
\blindtext[2] 

Another example.
\end{example}


\begin{example}[Yet Another title]
\blindtext[3]% 

Yet Another example.
\end{example}

\end{document}

Unless you relax your requirement to use layer files and style your layers using another method, I am not aware of a solution that meets all your requirements.

You do not need ArcGIS to read a file geodatabase (gdb) or to serve a WMS from it but my understanding is that there is nothing else that can read a layer file (lyr).

Another way would be to use package tocbasic coming with KOMA-script. You can easily set up a floating environment (or a nonfloating if you want to) using simple key-value pairs. All the listof-macros you know are there. The list will look just like your list of figures and tables (if you modified them a safe way).

You can style the environment using, for example, the caption package. If you are using package hyperref and its \autoref functionality, surprise ... works as well :-)

If you are resetting the counter each section, \thecounter will be longer making the output look ugly. Package tocstyle and it tocautoindent feature come to help. You need a few LaTeX runs till the needed space is calculated correctly.

\documentclass{article}%
\usepackage[tocindentauto]{tocstyle}
\usepackage{blindtext}
\usepackage{tocbasic}
\DeclareNewTOC[%
    type=example,
    counterwithin=section,
    float,
    %nonfloat, %If you don't want them to float
    name=Example,
    listname={List of Examples},
]{xpl}

\usepackage{hyperref}
%\hypersetup{hidelinks}
\begin{document}

\listoffigures
\listofexamples\clearpage

\section{Introduction}%
\begin{example}
    \caption{title}
This is the first example. The counter will be reset at each section.
\end{example}


\begin{example}
    \caption{example with ducks}
    Duck and cover!
\end{example}


\section{Quack}
Ducks are quite nice creatures, find a picture of a duck in
\autoref{xpl:duck}.
\blindtext[1]
\begin{example}
    \caption{More Ducks}
    \label{xpl:duck}
\blindtext[2] 
\rule{5cm}{2cm}
Another example.
\end{example}


\begin{example}
    \caption{funny penguins}
\blindtext[3]% 

Yet Another example.
\end{example}
\begin{figure}
\caption{figure}
\caption{figure}
\caption{figure}
\end{figure}
\end{document}

Using standard hyperref to show the link