I don't own both models, but when I finally decided to get my first autofocus camera I first bought a N90s, decided I didn't like it and went with the considerably (to me) more expensive F100 instead. Off the top of my head, I can remember the following differences:

-- I found the ergonomics of the F100 to be far more to my tastes than the N90s. That's purely subjective.
-- The F100 has a 96% viewfinder, the N90s has a 92% finder.
-- In manual mode, the F100 gives you two stops of metering feedback instead of just one.
-- The F100 allows you to set aperture in 1/3 stops on the camera instead of using the aperture ring. This also means it can use "G" lenses in manual or aperture priority mode.
-- The F100 supports VR
-- In S or P mode, the depth of field preview on the N90s always stops down to the minimum aperture. The F100 will stop down to the indicated aperture.
-- The F100 has a command dial on the vertical grip. (Not an issue for me, I don't own the grip!)
-- The F100 can autobracket with the standard back.
-- The F100 has Slightly more advanced matrix metering (Okay, I looked it up...10-segment vs. 8-segment)
-- I think the F100's shutter is rated for more shots.

Is it worth "trading up" at this late date? I'd say the two best reasons are a) VR, and b) is if you also shoot Nikon dSLR's. I find switching between the F100, D200, and D800 to be quite easy, with the controls falling to hand naturally. Nikon's also made some excellent new lenses in the last few years, but with the exception of the PC-E lenses they are all "G" designs without aperture rings.