Anyone who has ever owned a V3, TNT2u, or GeForce will tell you that the top gets almost as hot as the underbelly. The problem with cooling the top of the card, especially with AGP cards, is that there really isn't any way to effectively mount a passive cooling unit (like a heatsink) on it. The metal would not make direct contact with the chipset though the PCB, the base of the heatsink would risk damaging the solder contact points, and also, depending on the size of the contraption, would bump into your DIMMs or Processor. No doubt a few clever folks have devised a some pretty fancy work-arounds, but not without doing alot of work or modifications to the card.
This is what I recommend. It's cheap, fast to construct, does a pretty good job, and chance are, you probably already have all the parts.
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1. You'll need one CPU fan, preferably one with a 3pin connector so you can plug it directly into your motherboard. If not, the regular 4 pin connector is fine. It just looks neater with the 3 pin wire.
2. You'll also need two or three, plastic motherboard spacers as well. These are the little, white push though pins with the wide bottoms that you casted aside when you first got your motherboard. If you don't have any, they're a practically a dime a dozen at your local computer store or you can make up a substitute of your own. These pins will act as the "feet" supporting the fan.
3. Once you've fastened the pins onto the fan, either by use of superglue or other means, cut out a small section of double-sided tape for the foot pads. This tape is the same stuff that you would normally use for mounting pictures on the wall. After you've applied the tape onto the feet, carefully press it into place on the top of the card. Be very careful to not press the feet on top of any of the memory modules. The exact placement will be dependent on what card you have and what layout your motherboard is using as well.
The unit should sit level on the top of the card, but not stuck tightly. This is mounting is meant to be NON-PERMANANT. The tape should only be strong enough to hold the fan in place, but weak enough so you can remove it anytime you need to in order for you to work on your PC. Trust me, it won't move unless you toss the PC out the window.
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Viewing it sideways, you can see the supporting feet better (I apologize, but I don't have a better picture for it). You should try to get as much height as your motherboard layout would permit. On my particular setup, I'm only using two spacers. I recommend using only two spacers if possible as this provides less obstruction for the airflow, but if you find that the fan is too wobbly, go ahead and use three. I don't think you'll ever need four. You should also note that the fan does not have to be perfectly positioned over where the main video chip is soldered. Placing the fan just off to the side (see above) is actually better as it provides a more uniformed airflow across the chip's backside. This setup is also very effective in circulating cool air over the card's memory modules which is probably the biggest benefit of cooling the top of the card.