I was getting fed up with OneNote and Journal again, and after seeing a friend's law school notes program, I decided to see how hard it would be to write a replacement that fit my requirements exactly.
The short answer is that it's pretty easy to do something like Journal. Basically, there's a number of controls, but the InkCollector and InkOverlay objects are most useful. They can attach to any Win32 handle and turn it into a writable surface. Then you can go in and deal with the Ink as a whole down to individual strokes. You have complete control over the Pen and just about everything else, set through properties on the InkOverlay object.
That also means if you embed a WinForms control on an ASPX page, you can Ink-enable a website. Cool.
So, unless OneNote makes major strides in the final version or the Journal team decides to expose the API, and assuming I can find the time to work on it, I'll probably write a note-taking program for my classes. Maybe I can even tie it in to automatically generate outlines, etc. But in the meantime, I've decided to work on the InkBlogger application as a learning experience. It's a smaller, simpler application and, more importantly, if it fails it won't make me lose valuable notes!