[jbenny]

I tried Journal and OneNote for annotating other documents. I didn't like the fact that you have to "print" the document, which creates a graphic image of the original. It is this graphic that Journal and OneNote work with. For note taking, both programs are very nice.

You can also install ink addons to MS Office and deal with the documents natively. This requires a Tablet PC version of WindowsXP or Vista (yuck).

For annotating a PDF, I tried three different programs and bought PDF Annotator for the price vs features. PDF Annotator adds its annotations by adding a separate layer to the original PDF. There is no graphic conversion involved. You can also later remove that annotation layer if you wish.

If you are wanting to annotate an ebook, the best program that I have found so far is MS Reader (Tablet Edition). I don't like proprietary ebook formats (LIT, MobiPocket, Sony, IMP, etc.), but at least with LIT, you can "convert" and use it how you want. For creating a LIT yourself, there are several free tools.

For reading a variety of non-DRM'ed ebook formats, I think FBReader is the most flexible. I use it on a desktop PC, a Tablet PC and a Nokia N800 (Linux). It doesn't support annotations yet, but that and other features are coming. One tie-in with LIT is that if you "explode" a LIT ebook, Zip all the exploded files and then rename the Zip file with the ".oebzip" extension, FBReader will open this directly. Works great.

I haven't found the perfect all-in-one solution myself, but for now, these methods are workable for me.