Being able to use my iPad for taking my notes just like I did with paper and pen was the final straw that made me buy my iPad. I can type fast, but it always seems like I can write faster, and when I take notes by writing it helps me think about what I am writing and remember better.
However, everything I saw for the iPad looked like a crayon, and writing with a crayon was just not going to work for me. Then I found the Adonit Jot, it looks like a pen with a round plastic disk at the bottom, and best of all it writes like a pen.
I recommend you have a screen protector on your iPad screen, because dust and dirt can get under the plastic disk and possibly scratch your screen.
Below I have a video of this iPad pen, and the app I use Noteshelf which has been specially written to respond to the Adonit family of styluses which work on any touch screen device Apple, Android, and others.
Noteshelf was my choice because of the price $5.99, and it was so totally natural to use. Noteshelf has many features for both handwriting, highlighting and typing. As well as colored pens, and adjustable pen widths. If you need to find a page you can do that by typing text into the page or using the page browser which displays 9 pages at a time and lets you scroll through them so you can find the page you are looking for.
What is nice is you can take a picture and then import it into a page and then write on it. This is great for fill in the blank type forms or pages you want to save in a notebook. You can export your notebooks to PNG images or PDF files. For the stylish, you can buy different book covers, and page layout sets for $.99.