the ones that immediately come to mind are it won't meter with manual focus lenses, its autofocus only has 3 points (versus 11-51 on other bodies), mirror lock-up, no wireless flash commander mode, no gps input and more reliance on menus to configure it.

it also lacks more esoteric features such as 14 bit a/d converter, an intervalometer, individual lens calibration and an artificial horizon.

on the other hand, the d40/d60 can mount old non-ai lenses without risk of damage, whereas no other recent nikon body can do that. because of that risk, many people avoid non-ai lenses (or have them modified so they can be used), and they can be found for very little money.