Special characters like % throw href off. What package, if any, gives a work around? Would there be a side effect to changing the URLs from % to \%?
EDIT
On a second try, on a different computer, I do not see any problems except that TeXworks editor does treat items in a href after % as a comment (and actually so does this web site!) On the first computer I got an error message too. I'll post if I can reproduce it.
\documentclass{article}
\usepackage{hyperref}
\begin{document}
% the original URL
{\href{http://wims.unice.fr/wims/wims.cgi?session=1I6D03A2E6.5&+lang=en&+module=tool%2Fanalysis%2Ffunction.en}{ App 0.1 }}
% the modified URL
{\href{http://wims.unice.fr/wims/wims.cgi?session=1I6D03A2E6.5&+lang=en&+module=tool\%2Fanalysis\%2Ffunction.en}{ App 0.1 }}
\end{document}
\hreffrom theurlpackage then%is OK so long as the command is not in the argument of another command (that is, the same rules as for\verb) – David Carlisle May 31 '12 at 12:42\hrefso if you have such a macro it must be defined somewhere, but you have not given any indication of what definition you are using. url package is a common one, but hyperref and many classes also define similar but different versions. – David Carlisle May 31 '12 at 14:38%2indeed works with hyperref 6.82p, but (if my memories are correct) there are older versions of the package where it does not work. (\listfilesin the preamble of the document will list all files with version info at the end of the log file.) 2. Why don't you use/instead of%2F? That should work with all versions of hyperref, url or whatsoever. 3. Also UltraEdit (13.20a) treats everything after a%as comment, but tex.SE is at least so smart to treat text after\%not as comment. – Stephen May 31 '12 at 15:42