This post was very helpful, but I'm wondering if there's an update? I want to download, edit and/or annotate PDFs and then send them up to a web-based storage cloud. Is iAnnotate still the best way to do this? Have other apps come out recently or been updated recently that are better? And by the way, is there also an app that allows either annotating Word documents or supports the track changes function in Word?
Now that I have an iPad that is so mobile, I'm trying to become paperless by taking notes in meetings and editing or annotating documents using my iPad rather than printing them out and marking them up. But I may be asking too much.
I would take a look at Goodreader - excellent alround app and they have recently added annotation/highlighting for PDFs.
I haven't used cloud syncing but I imagine it will do what you need:
GoodReader for iPad for iPad on the iTunes App Store#