Yes, there is a big difference and the perldoc-style link seems to work well. It would be even better (you just knew that was coming didn't you) if it wasn't case-sensitive or if it redirected to search on failure. Eg: http://search.cpan.org/perldoc?LWP::Useragent simply ends up saying 'Not Found' simply because 'agent' was not capitalised.

Anyway, I've ended up getting sidetracked on the details of linking from PM to search.cpan (which arguably isn't broken anyway) when what I'm most interested in is setting up an infrastructure on PM so that search.cpan can link to discussion forums. I think the best approach (at least initially) would be to base the structure around distributions on the PM side.