Nikon supplies a mini-HDMI connector for playback on a TV, but the camera doesn't seem to scale photos intelligently when output this way. The lower cover hides the connector for Nikon's GP-1 hot-shoe GPS.
For compatibility with legacy lenses that don't have an AF/MF switch on them, Nikon includes an AF/MF switch on the D90's body--as it does on all its dSLRs. But you have to keep the switches in sync, making sure that both are in AF mode or both in MF mode, which is annoying. Furthermore, there's a warning in the manual that indicates you can actually damage the lens if you try to manually focus with the body switch set to AF.
You can assign a variety of useful functions to the Fn button, including direct-access to the different metering types and resetting to the center focus point. It's in a good location from a shooting perspective--it falls under the middle finger of your right hand--but if you don't know it's there, it's easy to overlook.
One advantage of jumping up a price class from around $800 to around $1,000 is that most of the models--the Rebel XSi is a glaring exception--retain the top status LCD. On the D90, pressing the Info button displays the same information on the back LCD.