Hated Jira and Confluence? Compared to what? Given that I find Jira to be perhaps the finest issue tracker I've ever worked with (compared to Remedy, Vantive, Scopus, RT, bugzilla and FogBugz), I would genuinely love to hear what tool you think is better than Jira? Particularly now that they can do advanced searching with JQL (Circa 4.x), I don't know of any tool that compares, particularly out of the box.

And, while sharepoint is a little more feature rich, and has better Office/IE Integration than Confluence, it also doesn't play particularly well with alternative platforms like firefox - I'd like to hear what your preferred Wiki platform is. I'm kind of a TWiki bigot personally, but if I had to drop a new wiki on a for-profit company tomorrow, it would probably be confluence.