D90 was 720p only, D3100 is 1080p, plus apparently better video controls, I say apparently because of what reviews say about the 3100, and I have the D90 and I know its many shortcomings, so the D3100 does have better video than the D90. Yes, D5000 looks to be the same as the D90, which is poor.

It's a moot point looking at prices. If the OP provided some prices they found, then it would be a simple exercise to help the OP rank the cameras.

Once we start venturing into D7000/7100, 3100/3200, 5000/5100 territory, you need to then start asking what video options you want. Do you want 24 and 30fps for each resolution, or only 24fps? What about the option for slo mo at 60fps? Some of these only do 24fps, which is a pain if you are editing and mixing videos of different fps sources. Do you want the flexibility to be able to shoot for different formats ie NTSC and PAL? What about audio recording options? What would the OP like?

It comes down to the budget and requirements of the OP, without knowing that we can discuss this for days.