I've seen a number of reports of special characters breaking links, some of which seem to get fixes, others seem to be tagged "status-by-design". I didn't see any indicating that the $ sign wasn't working so I thought I'd report it. I tried to link to:
http://c2.com/cgi/wiki$?VirtualPairProgramming
But the link does not appear as a link either in the editor or in the completed question. I fixed it by using TinyURL to proxy the link and pasting in the TinyURL.