Several comments have asked for my recommendations. After two days of tinkering, here is what you should do if you’d like to use your iPad to read and annotate PDFs.

* get the “iAnnotate”:http://itunes.apple.com/app/iannotate-pdf/id363998953?mt=8 app. Its UI needs a lot of work, downloading and uploading are clumsy, but it does a fine job of letting you read PDFs and annotate them, and those annotations are usable back on your Mac/PC.
* install the “iAnnotate PDF service”:http://www.ajidev.com/iannotate/index.html on your Mac or PC. This is a lightweight server that passes PDFs back and forth between your desktop and the iPad. Just point it at the directory where you have your PDFs on your desktop.
* on the iPad now in the iAnnotate app, you can connect to the desktop machine and download PDFs. Unfortunately one at a time. Please Ajidev, add batch transfer capability. UPDATE…hmm batch transfer seems to be happening now. Something I did wrong? Updated app? Either way, awesome.
* Annotate away on the PDF. Personally I use the highlight tool to mark a section, then select the highlight and add a note.
* When done annotating, upload the annotated version back to your PC. This is where the UI really blows. With the doc open in iAnnotate, hold your finger on the doc name in the upper left for a while. You will get no visual feedback. Lift your finger and a properties dialog will appear with an upload option. Upload away.
* Back on your mac/pc, your annotated doc will be in your pdf directory with the words “annotated” appended to the name.

This isn’t bad. It is all very functional. I’ve done 15 papers already and it is becoming natural. How can it be better?

* Integration with Web of Science or other paper sources. The Papers app on the iPad promises to let you download papers directly from WEb of Science and others (tho I can’t make it work with the UW ezproxy settings). This would be very nice.
* Integration with endnote??? I don’t know about this. I use Endnote Web within Web of Science and that works fine, I don’t know what else I need.
* Integration with Pages. Would be awesome to be able to slurp annotations and citations into the Pages app.
* Integration with Papers on the Mac? Don’t know, I’ve just installed Papers, and while I like its organization features, the lack of annotation capabilities makes me wonder if I will ever bother with it.