Personally I've forgone the whole stylus option on Android tablets and have opted to use a good keyboard like FlexT9, Swype, or SwiftKey to enter text. The value here is that text is searchable so I can later perform serches(more on this later). Pen taken notes will also be image based so they will take up much more space.
That said there are a few good Pen optimized note taking apps. I use
Gnote which has features for keyboard and Stylus. The nice thing about Gnote is it syncs with your Gmail account so you can later access your notes from a PC or other Android device.
Also a good app is also
Quil wich is optimized for taking notes with a stylus.
I would however recommend that you use something like Catch or Evernote to store your image based notes. These services OCR your notes so you can search them later