At Ning we use JIRA as our bug-tracking system (when we started a couple of years back we were originally on Bugzilla, but we switched to JIRA fairly quickly), and it's really a great tool, part of our development and release process really (I'll talk more about that in another post).

For intranet doc-keeping we have mostly been using Confluence (also from Atlassian) and it's good enough, but about a month ago I discovered Clearspace from Jive Software (the guys that wrote Wildfire, now Openfire) and we've been evaluating it since, well, really using it. It's a fantastic product, seamlessly integrating discussion boards with a wiki, simple ways to turning a discussion into a wiki doc, group and individual internal blogs, etc. Also, it has some nice features like searching inside PDFs that you uploaded.

Confluence is a bit more wonky than Clearspace, but it still does the job if all you need is a Wiki. However, for the combination of blogs, forum, and wiki docs, Clearspace wins hands down (except in one point: Wiki syntax in Confluence is better).

Regardless, depending on your needs, all great tools. Highly recommended!