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I think Kindle, because notes are automatically backed up (for Kindle Store purchases), optionally sync, & there are a couple of ways to export them. By contrast most other reading systems don't seem to even provide export capability (except for FB/TW sharing), which makes absolutely no sense to me.
Still Kindle is just a start, not the end. I'd like to be able to send my notes to someone else with the same book, or overlay those of someone else (author or critics etc.). Kindle has parts of this. But it needs to evolve to a standard exchange format so vendor and format considerations don't get in the way. We're probably years away from that though.
I don't think a physical keyboard is essential - I'm finding Nook's touch keyboard at least as productive right out of the box (and better than my iPod Touch because my fingers fit better), and that's without any auto-complete feature as you might find on a smart phone. But of course if you want to write novels on your ereader, that's a different requirement.
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