Currently, the regular expression used in auto_link_urls and, by association, auto_link, does not allow for parentheses in URLs.
While this is not a very common occurrence (nor proper, I don't believe, but I could be wrong), there are certain highly populated sites that use this format. Take Wikipedia, for instance:
http://en.wikipedia.org/wiki/Spr...(computer_graphics)
With the current implementation of auto_link, the link you get back looks like this:
<a href="http://en.wikipedia.org/wiki/Sprite_">http://en.wikipedia.org/wiki/Spr...</a>(computer_graphics)
This patch adds both opening and closing parentheses to the list of allowable characters for the path in the AUTO_LINK_RE regular expression.
P.S. This is my first submission, so if I've done anything wrong in the patch/ticket creation process, please don't freak out. :-p