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Before you go too far down this road, you need to look at:
- how well HWR works in Linux --- the best I've found is Cell Writer, which is awkwardly comb-based and doesn't allow connected writing
- how well emacs works when being controlled in a graphical environment w/ no keyboard available --- while I've oft' considered learning emacs, I prefer pen computers and haven't found it a good fit
My inclination for this sort of thing would be to instead use a LiveScribe and send the text files into emacs --- but I just picked up an Asus Vivotab Note 8 and am thrilled w/ it. If you remove the emacs requirement it would work quite well.
You might also enjoy reading Jerry Kaplan's _StartUp_ for a background on pen computing.
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