I'm using Yep! for organizing my Documents via OpenMeta-Tags (they're synchable via Dropbox). Yep uses Spotlight for indexing Documents so you're able to find fast. The cool part is that you can have a second organizational structure on the data level. (You're able to put PDFs where you need them, eg. project folders, and still find them in Yep!)
For bibliographys and stuff like that I use Sente. I search for all my PDFs with a certain tag in Yep and just add them one by one to sente. This works great for me.
Btw: Sente is also able to create a synced copy, which is great if you have different macs (like I do) and working longer on a paper or article.