Wow, an impressive bit of work, Alexander, and not much doubt about which app wins the prize at the moment. My transition has been first HandStory, then Plucker, and only recently iSilo, which I now use most of all. I think both Plucker and iSilo outstrip HandStory for the sort of uses you've been discussing here, but HandStory also has various other tricks up its sleeve (eg images as single files, but also various things that I haven't tried but are described in the HandStory online manual.
What's good is that we have a three-way competition (four ways if you count MobiPocket, which I probably wouldn't count) which seems to be spurring on improvements. And JPlucker looks promising.
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