For me, the focus motor is a must. Otherwise my Tokina 11-16mm is MF only (which isn't as bad as it sounds). Manual focus on DX is a bag of hurt in my opinion. I always seem to miss it.
The video mode on my D90 is nice I suppose, but truth be told, I've only ever used it once, and that was to learn how to use it. My lady filmed a Christmas video on it. I still, for the life of me, can't figure out why consumers want 1080p so badly. i can't even tell the difference between 1080 and 720 on my televisions unless I watch them side by side.
Swivel screens.... I'm split on this. They definitely add a little bit of bulk and reduce durability, but I also have a tendancy to shoot at ground level from time to time.
12 vs. 14 megapixels spread across 2 dimintions gets you about 8% more resolution... meh.
The D7000 looks like a pass to me unless you are a film profesional. Now if you threw a stop or two of high ISO performance as well... then maybe we can talk.
As for the D900, if it can match the high ISO performance of the D700, then I'd say the extra 12mp are worth the $400 premium over the D700 (IF you print large and IF you don't already have a D700).
I've just recently got to my happy place in terms of my FX lens line-up. So now I can think about this sort of thing.