edit: there are categories of software that have representatives that are more dysfunctional than Sharepoint. Still, Sharepoint is pretty much the worst document management/intranet package you can find.
Enterprise software can be surprisingly awful. blasdel's story is the best, but I remember being astonished that you could actually pay for version control software. The fact that said version control software didn't even have atomic commits but did, interestingly enough, run on its own proprietary file system was almost a Kafkaesque punchline.
I've seen some gibberingly awful Oracle web interfaces for HR stuff like entering time cards, but the worst was a "Software Life Cycle Management" thing that a client was using — a bizarre issue tracker with piles of inane baked in process.
When you logged in it would open a sole chrome-less popup window. You weren't allowed to be logged in more than once per account: one computer, one browser session, one window, one tab, period. There were no hyperlinks and only one URL — all the buttons POSTed a form with tons of parameters back to the same URL, with lots of state both in the session on the server and independently in cookies. You couldn't link to anything, it had a ridiculous taxonomy system, and the search was actively antagonistic to you finding anything. Most of the actual data worth looking at was in unindexed Word documents attached to the issues.