There's this one Linux app that I love called Xournal. It is the best tool for taking notes on a PDF that I've found anywhere. With this app you can type note on the PDF, highlight the existing content, and cut & paste. You can also draw on the PDF in 11 colors and 6 thicknesses.
I want someone to port Xournal to Android (if it hasn't been already). This app on an Android tablet would be the Killer App, and I am not exaggerating. Tablets were invented for what this app can do. This app by itself will make carrying the tablet around worthwhile.
Do you want to know how great this app really is? Tell me if you've heard of the Entourage Edge and its great note taking ability. Guess what? Entourage are using Xournal on the Edge becuase it is simply the best there is.
P.S. If someone can point me at an Android app that already has these abilities, please do. I want to use it.
P.P.S There's also a Windows version, and you can find it on the Xournal project page.