Protecting your \fbox in a section command (since it is fragile) allows for it to be used without problem:

\documentclass{article}
\usepackage{xcolor}% http://ctan.org/pkg/xcolor
\begin{document}
\tableofcontents
\section{\protect\fbox{hi}}
\section{\colorbox{green!25}{there}}
\end{document}
Alternatively, the etoolbox package provides \robustify{<cmd>} which can make <cmd> non-fragile:
\documentclass{article}
\usepackage{etoolbox}% http://ctan.org/pkg/etoolbox
\usepackage{xcolor}% http://ctan.org/pkg/xcolor
\robustify{\fbox}% Make \fbox non-fragile
\begin{document}
\tableofcontents
\section{\fbox{hi}}
\section{\colorbox{green!25}{there}}
\end{document}
Similar functionality is provided by makerobust. Also see the discussion What is the difference between Fragile and Robust commands? When and why do we need \protect?
\chapter{A \fbox{test}}or\section{A \fbox{test}}works without a problem, even if you include\tableofcontents. Would you be able to provide an MWE that duplicates the problem? – Werner Nov 12 '11 at 07:58