I've got a couple of recommendations. Pete's right about the manual—it's for rare occasions when you really want to learn exactly how some feature works. (I admit I have read it, but I'm a religious instruction manual reader).
In my opinion, the help files on the camera usually tell you enough. To see those, while you're on a menu setting, you hold the [?/lock] button (third from the bottom on the left on the D90) and it will bring up a description of what that setting does or when you might use it. And on the 920k-dot screens it looks like it's printed on paper.
One suggestion I have for the D90 is to turn off image review (it's the 5th setting in the Playback Menu—the one with the 'play' symbol). My reasons for suggesting this:
-if you ever want to review a shot you can still easily press the play button.
-having the image up after a shot causes all kinds of problems, for example you can't change the focus spot or change the ISO because those buttons are used for photo navigation while an image is up
-It saves on battery life. I don't have hard numbers, but it's something in the neighborhood of half again as many shots that you can get if you don't always have the LCD turning on to display the image.
Another suggestion I have is to set the Fn button (custom setting f3) to 'Access top item in MY MENU.' My Menu is such a handy feature because you put just the menu items you use most in it so you don't have to dig through all the menus finding them. I set my top menu item to change what the built-in flash does for creative lighting (the wireless flash control). This also lets me get into My Menu in two buttons one handed (R-middle finger press Fn, R-thumb press left on the directional pad).
If you're looking for a starting point, here is what's in my 'My Menu' (in this order):
e2 Flash cntrl for built-in flash
d10 Exposure delay mode
a1 AF-area mode
ISO sensitivity auto control
a7 Live view autofocus
f2 OK button (shooting mode)
One of my biggest gripes about the D100 was having to press so many buttons to get to the self-timer settings. Happy shooting, Nick and Anaxagoras!