iAnnotate
I spent several hours with iAnnotate tonight. The verdict: lots of capability, lots of weird, non-standard interactions, and lots of weird, non-standard UI elements. In other words, it feels like a Windows app.
The main thing I'd really like to be able to do is use two fingers to scroll and turn pages while in the highlighted or drawing tool. The fact that I can't stay in toolbar-less full screen and turn pages while highlighting is annoying. Add to that the fact that if I'm in full screen and I hold to get the context menu and choose the highlighter, when I tell it I'm done with the highlighter, it drops me out of full screen. Darn near infuriating.
And Dropbox support is a pretty big deal, although it'd be nice if treated Dropbox like an equal member of the PDF library rather than requiring a separate download process. And I'm not even sure if my annotation data is being synced back to the PDFs in Dropbox. Ideally it would, but I'm pretty sure it doesn't.
But it does support an impressive array of annotation types, and it's clear they gave some thought to what reading a PDF on the iPad is like (horizontal zoom locking is a really nice touch).