depends to a large degree on where you can fit them.
The thing to bear in mind is that what you want to achieve is a flow of cool air across the motherboard and around the drives - particularly the hard drive. If you have intake vents on the front of the case the fans (when placed at the back) will draw air across the board. The CPU and probably the graphics card, will have their own fans, and these will be exhausting warm air into the case - although some high-end graphics cards have their own exhaust vents that take the heat out through the back of the case.
Air flow across the whole board is what to aim for, and remember that hot air rises - the top of the case will warm up, and you shouldn't stack anything on it. I've seen many a PC with a nice thick pile of old magazines on the top.