Well this is an old thread that seams to have resurfaced... so I hope I don't state the obvious....
But for cooling the case, what I did was install a Digital Doc 5 in the case which controls 5 fans.
Fan 1 - In the Digital Doc, really doesn't do anything. Pulls air from car to inside the comp. case.
Fan 2 - 120 mm, fan on the left bottom of the case, pulls air into the comp case from a hole in the car floor, so it pulls in outside air. A lot cooler than the case or inside the car.
Fan 3 - Blows directly on the HD.
Fan 4 - 120 mm on the right bottom of the case. Blows air out of the case through a hole in the car floor to the outside.... Exhaust the heat from the case basically and not into the car.
Fan 5 - In the dash behind the LCD. Just to get some circulation up there. If I have problems with being to hot for the LCD I will hook into AC duct.
The Digital Doc is the way to go (if you have a large case) cause all the temp. sensors and control circuits and setting ability is already there. Plus the display looks cool on the face of a case.
Just a note my case is about 17" deep, 38" wide and 15" high. It sits in the back on the floor board under the hatch of a C4 vette, so I have plenty of room for stuff like this, you may not, but if you do it seems like a decent approach to me.
Peltier's are neat things, but unless you exhaust them to the outside (of the car) you are wasting your time....