Dear Aunt TUAW,
I am in love with my iPad 2 and am eager to turn my upcoming trip to the beach into a working vacation. I find the that the PDF support in iBooks leaves a lot to be desired. Which is unfortunate, as I have spent a lot of time uploading a lot of PDFs into my iTunes to have them handy when I want to get work done. Is there a PDF annotation app out there that can access the PDFs I have stored in iBooks? (I realize that iBooks can't actually display PDF annotations, at least at present, but if I could at least quickly import PDFs into another iOS app, that would be a start.)
Your loving nephew,
Your problem is that you're reading PDFs in iBooks instead of Good Reader, PDF Expert, or any of the other multitudes of wonderful PDF clients that can display and edit annotations.
Unfortunately, no, you cannot directly share PDFs out from iBooks to other applications but you can import them in iTunes when you're home at your computer using the device Apps tab. That's the "direct" answer. There is, however, a sneakier solution that gets around iBooks' "Roach Motel" mentality (i.e. documents check in but they don't check out).
If you really need to transfer those PDFs when on-the-road, you can use iBook's built-in e-mail sharing to send a copy to yourself and then use your iPad's "open in" feature from Mail to send the PDF to the app of your choice.
Another good solution is to place all your PDFs into Dropbox/Box.net/Cloud app/Google Docs etc to ensure that your files can be accessed, read, and edited from all your devices.
The reading experience may not be as lovely in these other apps, but you'll be able to get your work done.