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Blackboard (if your school supports it)
Dropbox (for syncing files and for QuickOffice doc saving)
QuickOffice HD (for typing)
Notability (for handwriting, don't use it much)
Evernote (store all my class notes and notes I type)
 
I tried many apps but my workflow became

Notability - in classes without pdf lectures

GoodReader - in classes with pdf lectures

Pages - for word processing

Dropbox to keep my dropbox in order

iAnnotate does render pdfs faster than Goodreader, however I didn't like its interface or its file management/syncing system. Its useful to review pdfs you create in goodreader.

One huge advantage Goodreader has is that for handwriting it has the zoom box and the handwriting system in general is very smooth.

You might also want Keynote for presentations. For science journal articles I normally use Mendeley's Paper on my Mac however the Ipad version is lacking so I kept the Mendeley Folders synced to dropbox and synced those onto Goodreader.
 
Yeah iStudiezPro really helped me get organized. WolframAlpha is the best app I have ever bought. Mind blowing what it is capeable of computing. I refer to as the star track computer.
 
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