list of occurences of references

There are some adjustments to be made. Here's something that should work

\documentclass[12pt]{book}

\usepackage{amsthm}
\usepackage{environ}
\usepackage{imakeidx}
\usepackage{refcount}
\usepackage{hyperref}

\makeindex[intoc]
\makeindex[name=goals,title=Goal References,columns=1,intoc]

\newcommand{\gref}[1]{%
   [Goal~\ref{goal:#1}]
   \index[goals]{Goal~\getrefnumber{goal:#1}!Section \arabic{chapter}.\arabic{section}}
}

\makeatletter
\newcommand\l@goal[1]{%
  \addpenalty{\@highpenalty}%
  \vskip \z@ \@plus \p@ 
  \begingroup
  \parindent\z@
  \rightskip\@pnumwidth
  \parfillskip-\@pnumwidth 
  \leavevmode #1\nobreak\hfil\nobreak\null\par 
  \penalty\@highpenalty
  \endgroup}

\newcommand{\egregaddtocontents}[1]{%   
  \addtocontents{toc}{\protect\l@goal{#1}}}

% arrange goal numbering by chapter
\newtheorem{Goal}{Goal}[chapter]

% define a shorthand to be able to get at \BODY with \expandafter    
\newcommand\indexgoal[1]{\goalindex[goals]{Goal~\theGoal!#1}}
% save a copy of \index
\let\goalindex\index
\NewEnviron{goal}[1]{%
\begin{Goal}
   \label{goal:#1}%
   % here we neutralize \index so that it won't do damages
   \begingroup\renewcommand\index[2][]{}%
   % but the main command uses \goalindex, so it's safe
   \expandafter\indexgoal\expandafter{\BODY}%
   \egregaddtocontents{\BODY}
   \endgroup
   %{\em label:} #1 %comment in/out to restore/suppress printing label
   \normalfont{}\noindent
   \BODY
}
[\end{Goal}]
\makeatother

\begin{document}

\tableofcontents{}

\chapter{First}

\tracingmacros=1

\begin{goal}{firstfirst} 
learn more \LaTeX
\end{goal}

\tracingmacros=0

\begin{goal}{firstsecond}
spend time on content, not \LaTeX
\end{goal}

stuff\index{stuff}

\chapter{Second}

\begin{goal}{secondfirst}
have fun in any case\index{fun}
\end{goal}

Chapter contents here, referring to some goals:
\section{whatever}

Reference to a chapter 1 goal: \gref{firstsecond}

Reference to a chapter 2 goal: \gref{secondfirst}

\section{another}

Second reference to a chapter 2 goal: \gref{secondfirst}

\printindex[goals]
\printindex

\end{document}

I've used refcount and \getrefnumber, otherwise \index would produce different entries.

This is so close to a complete solution, built following Holle's index suggestion and using egreg's imakidx package, that I decided to post it as an answer rather than as an edit to the question. Still missing:

• the ability to expand the \BODY macro from the environ package inside the call to \index,
• guarantee that the expanded \BODY always appears first under its goal in the Goal References index, Edit: starting the index with a blank space before \BODY fixes this. Incorporate in in egreg's accepted answer.
• single column output for that index. Edit: deleting idxlayout package fixes this.

Here's the output from the MWE below, which isn't quite "minimal" since I need to make sure that other features still work.

\documentclass[12pt]{book}

\usepackage{amsthm}
\usepackage{environ}
\usepackage{imakeidx}
\usepackage[totoc]{idxlayout}
\usepackage{hyperref}

\makeindex

%% columns=1 isn't working
\makeindex[name=goals,title=Goal References,columns=1]

\newcommand{\gref}[1]{%
   [Goal~\ref{goal:#1}]
   \index[goals]{Goal~\ref{goal:#1}!Section \arabic{chapter}.\arabic{section}}
}

\makeatletter
\newcommand\l@goal[1]{%
  \addpenalty{\@highpenalty}%
  \vskip \z@ \@plus \p@ 
  \begingroup
  \parindent\z@
  \rightskip\@pnumwidth
  \parfillskip-\@pnumwidth 
  \leavevmode #1\nobreak\hfil\nobreak\null\par 
  \penalty\@highpenalty
  \endgroup}

\newcommand{\egregaddtocontents}[1]{%   
  \addtocontents{toc}{\protect\l@goal{#1}}}

% arrange goal numbering by chapter
\newtheorem{Goal}{Goal}[chapter]

\NewEnviron{goal}[1]{%
\begin{Goal}
   \label{goal:#1}
   \index[goals]{Goal~\ref{goal:#1}!BODY here}
   %{\em label:} #1 %comment in/out to restore/suppress printing label
   \normalfont{}\noindent
   \BODY
   \egregaddtocontents{\BODY}
}
[\end{Goal}]
\makeatother

\begin{document}

\tableofcontents{}

\chapter{First}

\begin{goal}{firstfirst} 
learn more \LaTeX
\end{goal}

\begin{goal}{firstsecond}
spend time on content, not \LaTeX
\end{goal}

stuff\index{stuff}

\chapter{Second}

\begin{goal}{secondfirst}
have fun in any case\index{fun}
\end{goal}

Chapter contents here, referring to some goals:
\section{whatever}

Reference to a chapter 1 goal: \gref{firstsecond}

Reference to a chapter 2 goal: \gref{secondfirst}

\section{another}

Second reference to a chapter 2 goal: \gref{secondfirst}

\printindex[goals]
\printindex

\end{document}