Ben Brooks recently wrote about the using the Griffin stylus for handwriting on the iPad. I agree with much of his post, but one thing I have discovered is that the stylus really makes the difference. I've tried several (but not the Griffin). A nice comfortable stylus is much better than using your finger for taking notes. Additionally, a stylus with a rubberized tip is key. It provides a subtle resistance against the glass that feels more like writing on paper. It's still much more slick than the sensation of writing on paper but better than the foam end on some stylus devices.
My personal favorite is the The Acase Capacitive Stylus (associate link). There are several versions. Most come with an attached plug that fits in the headphone jack of the iPad that attaches the stylus to the device. My personal favorite is the combo stylus that includes a ballpoint pen. It's also slightly longer than the standard version. I am still baffled as to why no one makes a full pen-sized stylus though. The biggest downside is the small size of the stylus in the hand.