kukkurovaca on the Lifehacker comments: 
"[this software] basically requires me to reroute my thought processes around an assumption which is not native to them; I don't think in chunks -- no matter how freely associated -- but in streams, to which I apply (or from which I induce) structure after the fact. This, I suppose is where paper notebooks continue to outclass electronic text-organizing systems despite all their apparent advantages."
He sounds like he needs an outliner. You probably do too. Get one!
Outliners work with you whether you think in chunks or streams. It's a simple tool that gives you Heinz's "57 Varieties". Stir in some connectedness, and you'll wonder why you ever used anything else. As for word processes, get yourself LyX.
Update: Response.
