I have tried a very wide variety of notetaking apps since the early days of iPad 1, then iPad 2, and now iPad 3. I use it heavily in my mathematically oriented work for annotating pdf files and generating my own notes, primarily via handwriting.
At first, Note Taker HD seemed the best, but it has since been overtaken by others. I think Note Taker HD still has the best vector graphics drawing tools (for a primarily note taking app, that is), but in most other respects GoodNotes has become my first choice. It just had an update, ehich immensely improved it. It has the (argueably!) best zoom window for handwriting, and the annotation and navigation capabilities are great.
Just wanted to share my reactions with you.