Onenote. For me the killer feature is the ability to put text wherever i want, and move it later, i just click where i want to write in the page and type, it really changed the way i take note, it feel more natural and more close to the "paper experience". i tried opensource solution, but all the one i found allow only for "linear" note taking, witch is ok if i need to take a quick note, but if i need to "prototype"…
Really like OneNote too. One geature it really lacks though is real tagging (#hashtags).
Ideally keep the current system (ctrl+1 to cycle through checkbox, checked checkbox and nothing is nice) but add tags on top.
(If they have added tags and I haven't realized then I'll be happy to know.)