Iíve been trying out Voodoopad for the past week and found its really good at fast notes ; links from index page to note pages, imports or links with photos, links for HTML and PDFs (spawns external viewers Safari and Preview). The lite version is free. The full version ($30 US) supports a sketchpad.
But I just acquired a Newton, so we'll see how that goes! (in the "More Stuff than I Really Need" category.)
Congratulations! Which model of Newton do you have? I have a MessagePad 2000 sitting around with tons of goodies... If only it could get it to sync my notes with something properly on the Mac I would still be using it. I enjoy pulling it out though just to marvel how much ahead of its time it really was. It's the ultimate note taker in my opinion.
I also vote for Sidenote. It's really handy to have it slide in from the side of your screen whenever it's needed. Plus it does a good job of organizing your notes. It looks good, has a lot of features and, perhaps best of all, is free.
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For note-taking in class i use MS-Word and open blank documents (on a MBP). I find its easy to navigate and format things on the fly to my liking. I havn't had to place pictures or links yet, however I can't see it being difficult.
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