Which motor is getting hot enough that you need to cool it?
For the non-CIMs:
Either the motor is poorly vented, or you're pushing too much current through it. A poorly vented motor can easily be resolved via uncovering the vent holes, adding washers to the mount screws so the vents get more air, or allowing more air to flow to the area where the motor is. This depends on which specific motor it is though, as the varying motors have different vent holes & methods of staying cool.
If you're pushing current through it, I'd presume that the output torque on the motor is closer to stall than it should be. Long story short, you either need to reduce the load you're trying to lift/push/whatever, or add another motor.
For the CIM motor, well those things can take a beating. There's a picture floating around here where someone took a thermal image of them after a match -- they were 140F! (Almost hot enough to fry bacon
). Unless you're lifting a massive load that really is pushing them towards stall, then I wouldn't worry too much.
Search the CD-Media link at the top for "JVN Calculator", and use that spreadsheet as a sort of guide to figure out if you're drawing too much current. Remember, if you stall a motor too many times it will simply burn out.