Plain old word doc by chapter here and extensive excel sheets for characters, chapters names/goals/word count. Also keep a 'to do' list while re-reading or editing. I use Toshiba bulletin board working off flash drives, which is effective and easy and also allows the addition of images etc. Then I keep a steno pad (or more) for every manuscript where I doodle and work out complicated world info. (I back up on two separate computers as well.) That system works well for color highlighting certain things and for shrunken manuscript work, which I find crucial.
I believe that the Google cloud will be my final home, but for now--I don't have the hard control I want to have on the editing process there.
Some downsides: Once I compile it into the single manuscript after I've gone through several drafts--live gets complicated. As I set up pages for agents etc i can't keep from tweaking, and those tweaks don't always make it back into the original manuscript. (Not sure they should--often times the tweaks are god-awful mistakes.) Problem is that I start to get confused on which is the most recent vetted pages and are they in the single manuscript or not? I don't know if other writer programs would solve that or not. Generally those are e-mails that I save, so they are located on a whole different platform.
I keep everything, labeling chapters 01.23 (Chapter 1, rewrite 23 etc) for example. I tried Scriver beta, but it was more complex than the system I've in place. I don't like to fight a system while I'm writing. Also, my Toshiba has a cool bulletin board that is excellent, but over time the short cuts can get lost and I have to relocate and reattach--especially when I do my year end back up into a safe deposit box. That bulletin board though gives me one central location to easily click back and forth.
I do know that Jim specifically mentioned that he didn't recommend any particular program, and I think that he uses a word type program. He does love his giant poster board for plot work etc. That's in his writing journal.