GoodReader plus Papers and the Mac version of Papers. Killer combo.
+1
I'm in biomedical research and have used Papers for years-- it's a stellar app, my Mac-based grad students really like it as well.
I'm in the middle of writing a review and traveling a ton, so I have the refs I am using all synced with my iPad -- has both cut down on the paper I drag around and also gives me piece of mind that I won't forget a crucial reference, an all-to-common and frustrating occurrence.
I'm looking forward to the future refinements, including annotation.
Bottom line is that it is a *great* desktop app and the iPad is a nice adjunct to it.