On this question I was trying to put a link in a comment. The link is en.wikipedia.org/wiki/RSA_(algorithm). But the end parentheses isn't part of the link. Is this a bug, or am I just doing something wrong?

Instead of the plain link like you used (http://en.wikipedia.org/wiki/RSA_(algorithm)), you can use the markdown version:

[RSA](http://en.wikipedia.org/wiki/RSA_(algorithm))


I used my moderator powers to edit your comment this way.

Of course, this still works only when the parenthesis are balanced in the link - otherwise use the URL-encoding as proposed by Maeher's answer.

You can just encode the parentheses, then it works: http://en.wikipedia.org/wiki/RSA_%28algorithm%29

See URL detecting error with address like "http://en.wikipedia.org/wiki/Octet_(computing)" on Meta Stack Overflow for details; long story short: After the next build of the site, this will work as you had expected.