To be honest, neither the 600 nor the nook will give you all that wonderful a reading experience for your school PDF. The screens are too small and most PDF are made for a letter sized page. What I would try is some of your PDF on a Sony PRS-900 and see what you think of that. i cannot say if it would be good enough or not. Only you can say. You can put your PDF on an SD card and try it on a 900 when there is a demo unit at the local SonyStyle shop.
And there is also the KindleDX that moght be ok for your PDF needs as well. But the PDF support does not include links or ToC.