Here is one option provided via a \colorcaption for each of the coloured figures:

\documentclass{article}
\usepackage{etoolbox}% http://ctan.org/pkg/etoolbox
\makeatletter
% See https://tex.stackexchange.com/q/113147/5764
\catcode`\#=12
\newcommand{\colorcaption}{%
\patchcmd{\@caption}{\par}{%
\par\addcontentsline{lcf}{#1}%
{\protect\numberline{\csname the#1\endcsname}{\ignorespaces #2}}}{}{}\caption}%
\catcode`\#=6
\let\@oldstarttoc\@starttoc
\newcommand{\listofcolorfigures}{{%
\renewcommand{\listfigurename}{List of Coloured Figures}%
\renewcommand{\@starttoc}[1]{\@oldstarttoc{lcf}}\listoffigures}}
\makeatother
\begin{document}
\tableofcontents
\listoffigures
\listofcolorfigures
\section{A section}
\begin{figure}\caption{A figure}\end{figure}
\begin{figure}\colorcaption{A colour figure}\end{figure}
\begin{figure}\caption{Another figure}\end{figure}
\end{document}
The idea is to create a \colorcaption macro (for coloured figures) that acts the same as \caption, but also inserts a contents line into a new ToC file (with extension .lcf - for list of coloured figures). A companion \listofcolorfigures acts just like \listoffigures, except it calls \@starttoc{lcf} to generate the list of coloured figures.
Patching an argument inside a macro requires some assistance, as provided by Patching arguments inside a macro.
figure, also adds itself to its own 'list of' (see the TeX Blog or thetocloftpackage). – Sean Allred Sep 23 '13 at 04:37