I use
Handnotes when I want to write things out in my own handwriting and draw things along with it. It works pretty good and you can organize notes by topics (i.e. school, work, personal, etc.) This program sounds exactly like what you are looking for.
Another program I just started using is
PhatNotes that works extremely well with Pocket Informant and syncs with outlook notes. But I don't know too much about it. I'm not even sure if you can write in your own hand writing. I mainly use it for taking notes that I use calligrapher to enter.
When I am taking long notes I use Word, but am looking at textmaker.