uPad on the iPad works pretty well for me for this though having tried a few different apps I quickly became aware that individual workflows and requirements vary massively for the seemingly simple requirement "taking notes on pdfs".
I've got a cosmonaut stylus which I'm pretty happy with on the iPad.
Broadly speaking I don't like a the idea of a tablet with a stylus as it would be better for a small number of use cases but worse for a far larger number.
The screen doesn't handle detail brilliantly for handwriting but uPad gets round this by giving you a larger writing area which it then shrinks onto the actual document. Basically you write an inch high and it crunches it down to about 40% of that. It works pretty well, though I'd still use the keyboard for significant text input - it's completely workable once you get used to it.
