Another approach always using TikZ.
Since the backgrounds library was not exploited so far, I made use of it; first I defined two commands that allow to fill the background of the elements highlighted or not:
\NewDocumentCommand{\highlight}{O{blue!40} m m}{%
\draw[mycolor=#1] (#2.north west)rectangle (#3.south east);
}
\NewDocumentCommand{\fhighlight}{O{blue!40} m m}{%
\draw[myfillcolor=#1] (#2.north west)rectangle (#3.south east);
}
corresponding to the styles:
\tikzset{mycolor/.style = {line width=1bp,color=#1}}%
\tikzset{myfillcolor/.style = {draw,fill=#1}}%
Inside the document, to highlight some elements of the matrix, it must be used the environment pgfonlayer with a dedicated background layer myback:
\pgfdeclarelayer{myback}
\pgfsetlayers{myback,background,main}
Then it is possible to call:
\fhighlight{m-1-1}{m-3-3}
or
\highlight[red]{m-2-2}{m-4-5}
The complete example:
\documentclass{article}
\usepackage{xparse}
\usepackage{tikz}
\usetikzlibrary{matrix,backgrounds}
\pgfdeclarelayer{myback}
\pgfsetlayers{myback,background,main}
\tikzset{mycolor/.style = {line width=1bp,color=#1}}%
\tikzset{myfillcolor/.style = {draw,fill=#1}}%
\NewDocumentCommand{\highlight}{O{blue!40} m m}{%
\draw[mycolor=#1] (#2.north west)rectangle (#3.south east);
}
\NewDocumentCommand{\fhighlight}{O{blue!40} m m}{%
\draw[myfillcolor=#1] (#2.north west)rectangle (#3.south east);
}
\begin{document}
Using the \verb!myfillcolor style! (\verb!\fhighlight! command):
\[P=
\begin{tikzpicture}[baseline=-\the\dimexpr\fontdimen22\textfont2\relax ]
\matrix (m)[matrix of math nodes,left delimiter=(,right delimiter=)]
{
0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 1 & 0 & 0 & 0\\
0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 0\\
0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 1 & 0 & 0 & 0\\
0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 0\\
0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 1 & 0 & 0 & 0\\
0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 0\\
};
\begin{pgfonlayer}{myback}
\fhighlight{m-1-1}{m-3-3}
\fhighlight[green!30]{m-3-9}{m-5-13}
\end{pgfonlayer}
\end{tikzpicture}
\]
Using the \verb!mycolor style! (\verb!\highlight! command):
\[P=
\begin{tikzpicture}[baseline=-\the\dimexpr\fontdimen22\textfont2\relax ]
\matrix (m)[matrix of math nodes,left delimiter=(,right delimiter=)]
{
0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 1 & 0 & 0 & 0\\
0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 0\\
0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 1 & 0 & 0 & 0\\
0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 0\\
0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 1 & 0 & 0 & 0\\
0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 0\\
};
\begin{pgfonlayer}{myback}
\highlight[red]{m-2-2}{m-4-5}
\highlight[orange]{m-5-7}{m-6-9}
\end{pgfonlayer}
\end{tikzpicture}
\]
It is even possible to highlight single elements:
\[P=
\begin{tikzpicture}[baseline=-\the\dimexpr\fontdimen22\textfont2\relax ]
\matrix (m)[matrix of math nodes,left delimiter=(,right delimiter=)]
{
0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 1 & 0 & 0 & 0\\
0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 0\\
0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 1 & 0 & 0 & 0\\
0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 0\\
0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 1 & 0 & 0 & 0\\
0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 0\\
};
\begin{pgfonlayer}{myback}
\foreach \element in {m-1-1,m-6-5,m-5-3}{
\highlight[violet]{\element}{\element}
}
\foreach \element in {m-3-10,m-4-8,m-5-12}{
\fhighlight[violet!20]{\element}{\element}
}
\end{pgfonlayer}
\end{tikzpicture}
\]
\end{document}
The result:

!in front of it to turn it into a link. A moderator or another user with edit privileges can then reinsert the!to turn it into an image again. – Martin Scharrer♦ Jan 4 '12 at 13:57