Web Worker Daily has a good post on PDF Tools. The list of 15 tools is by no means complete, but it's a pretty good start (and more tools keep being mentioned in the comments). I'm not going to name the programs WWD missed; instead, I'll post a comment over on their blog.
Aha. I went digging through my bookmark folder and I found another list from January 2009. This list is made up of specific needs and the app that fills the need. It's older, though, so some of the links are probably dead.
P.S. You probably want to bookmark the 2 links.