Like Nokia said you can either connect an extra fan to your mobo using a three pin fan connector, it's imprtant to connect it correct, cause one pin is used for monitoring the other two for voltage. Or you can connect a fan to a normal molex power cable, this can be done using a fan with a four pin molex connector, or with a cable that goes from 3 to 4 pin.
The negative side about connecting the extra fan to the mobo is that the power comes trough mobo, extensive power demands are not recommended for some motherboards, the positive side is that you will be able to monitor the fan, set sleep mode, make the fan produce less noise by rpm adjustments, keep a spare molex.

If it is your AGP card that is getting hot, see to replace the heatsink / fan combination.
You have an onboard VGA solution? Than it's probably that chip or your connection between the chip and processor (AGP bus and or chipset bridge) that's heating up. See if heatsinks are attached to your onboard video, if not install one!
You can also install either an extra intake fan in front or an exhaust fan at the back.
(see for not so noisy cooling solutions my basic cooling and noise tutorial at AntiOnline.)