Notebook
Used Circus Ponies' Notebook for one of my midterm exams. On one page I would copy and paste from PDF notes (from Skim) or type out notes from my hard copies and class notes. On the other page I would write my responses to the exam questions. I could open the note pages in their own window so I could easily reference them as I typed. As a visual person, this interface really worked for me and made compiling notes fun. From Circus Ponies' site:
With NoteBook, you organize your information naturally, using a familiar notebook interface, complete with pages and tabs, sections and subsections. Add notes and other text. Drag in files and folders. Even "clip" web research, mail messages and other content into your Notebooks without leaving the application you're working in. Annotate your information with diagrams and sketches, highlighting and keywords. Take voice-annotated notes that you can download to your iPod. And protect private thoughts with passwords, covers, and encryption.