If you have been looking for a note taking app that allows you to type as well as write, you might want to check out Noterize. [Right now 2011.07.02, it is FREE. Before you download, make sure the price has not changed.]
You can watch a video here.
The app allows you to view and annotate PDF and powerpoint documents. The built in web browser allows for direct importing of readable files from the web. You can even record audio notes. There is also Dropbox and Box.net integration.
Built in search functionality lets you find what you are looking for quickly.
You can even share pages with friends via social sites or email. The built in password protection can help keep notes secure.
iPad Notebook 
I accidentally deleted noterize from my iPad and now that I re-enstalled it, I can’t get my notes back…. any suggstions?
If you made a back up of your iPad using your computer or iCloud, the notes may still be there and you can then bring them back. You may need to check with the app developer about how to access the backup. Good luck.
This app is now called Paperport and is currently still free.
I think is the best app yet. However, I cannot find it any more in the app store.. not even as paperport. I need to sync what I do on Noterize in my iPad to my miniiPad. Any ideas? I tried to sync the ipad and then the mini but it will not copy the changes made to the document in the ipad to the mini ipad.
See if this is the link you are looking for. The product is called PaperPort Notes. It was updated last December 23, 2012.
help! yesterday I suddenly lost access to my notes in notarize. I have important notes and recordings of lectures I need. I get an error message, and cannot open the app at all!
Also, there was a thread on an Apple discussion board that may be helpful if you cannot get in touch with the developer.