Interesting article over at Wired on Trent Reznor's work flow for How To Destroy angels. It's a step-by-step for a track and includes snippets of the work in progress. I thought the inital step was really great: Reznor and his producer work on two totally different projects then see what happens when they chop and change between then. Nuts. But you can totally hear how it ends up in the song.
I also read somewhere about KTL doing something very similar, with much less song-like results.