The iPad app GoodReader allows you to annotate on top of PDF files, this page will give some tips and tricks for editing the content of PDFs on desktop systems.
From super-effective search tricks to Google tools specifically for education to tricks and tips for using Gmail, Google Docs, and Google Calendar, these tricks will surely save you some precious time.
Elementary school iPad app recommendations via the Department of Educational Technology in the School District of Palm Beach County iPad Pilot Project wiki
Some teacher apps, some students apps, some free, some paid.
Wouldn't say they are the "10 best" but the list definitely offers some interesting app information.