No ability to use a custom prefix, like KEN_0123.JPG, for the file names.
No Mirror-up mode. This mode sucks in the D3, D700 and D300 anyway.
WB/ISO/QUAL buttons shared with other functions, but still easier to use than the hidden ones on the D3, whose locations date from the F5.
No option for seeing the Focus Point Selection in playback, but who cares?
No Intervalometer (automatic timed shooting).
Can't set ISO or exposure in full stops: ISO sets only in third stops, and exposure only in third or half stops.
No ability to change the focus and release priorities in the AF-S and AF-C modes.
No metering, finder read-out or EXIF data with manual-focus lenses. (buy a
small light meter and a hot-shoe adapter if you can't use the LCD to guess exposure.)
No macho-man metal body, so the D90 weighs much less. The D90 has a metal lens mount.