The Papers software in Mac is really good!! http://mekentosj.com/papers/
I am mainly using Windows, are there similar alternatives?
Mendeley is similar (and cross-platform), thought it lacks some of the polish. It also has collaboration and syncing built in.
I also really enjoy using the Firefox add-on Zotero.
There is now also a Windows version for Papers (pre-release for now, Feb 14th 2012): http://www.mekentosj.com/papers/win
(disclosure: I work with Mekentosj)