> So I think that LaTeX2HTML definitely has it right here.

yes and no.

The following works in latex, but presumably not in latex2html


\documentclass{article}
\usepackage{makeidx}
\makeindex
\begin{document}

percent\index{%@\%}
\printindex
\end{document}

note that you might want to do that, rather than just use \% as then
the entry gets automatically indexed in the right order.

However the fact that \index reads some characters verbatim is, like
all verbatim things, a thing or rather dubious merit. Since you can't do
\section{percent\index{%@\%}}

What latex2html should do about that I don't know. Probably nothing:-)

David

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