The decision is a bit tricky because you have a number of decision points. You're also excluding both Sony and Panasonic, both of which are better than Nikon or Canon for video.
I'm in a similar boat in terms of upgrading from the D40, and am considering the D7000 or D5100, which is essentially a choice between the lighter weight, articulated screen, and lower cost of the D5100 versus the flexibility, better viewfinder, and better AF of the D7000.
In general, if still photography is your most important reason for getting the camera, and you're going to pull focus when using video, then Nikon or Canon work well. The decision point there would be whether you need 60 fps. That one is actually fairly easy.
The complication comes if still photography is of lesser importance than video, especially if you'd like the ability to switch seamlessly between stills and video or want autofocus that really works. If that's the case, then I'd look at the Sony A55 and Panasonic GH2. Both have huge electronic viewfinders that work for both stills and video. While they're both fairly good taking basic still shots, however, they're not as good as Nikon or Canon when using flash or in low light, and don't have the wide range of available lenses either.