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Before you hop online and buy the fastest graphics cards you can get your hands on, make sure you're picking the models (and motherboard) that facilitate proper airflow.
Your best bet is on a card able to exhaust the heat it dissipates straight out the back of your chassis, even if its blower-style cooler tends to generate more noise. Typically, the reference models designed by AMD and Nvidia are good examples, though the Radeon HD 6990, GeForce GTX 590, and lower-end GeForce cards are guilty of deviating from our direct-exhaust preference.
This is what happens when too much heat builds up. A mesh grill where those closed slot covers are seen might have prevented the card's label from getting so hot that it warped. Learn from this mistake, though. Eight hundred watts of heat dissipating in this chassis was bound to have adverse effects.
As long as the graphics card can get the heat out of the case, temperatures will stay at acceptable levels. Even a multi-GPU array has access to enough airflow to operate within safe tolerances, so long as there's room to breathe between the GPUs. If you want to exploit the value benefits of CrossFire or SLI, buy a motherboard with at least one expansion space between installed dual-slot cards (that's two vacant slots between the two end up using).
If the cards are too close together, as in the image above, it's easy for the board blocked off to overheat under even moderate duress. After all, its fan can't draw in enough air to keep the graphics processor cool.
The situation is similar when it comes to dealing with graphics cards sporting axial fans. Though they're quiet, they end up blowing hot air around inside of your case, rather than out of it, leading to undesirable heat build-up.
In many cases, a side fan can help. Even though they're continually criticized in our forum, a side fan's effectiveness (and the subsequent improvement to graphics card cooling) is both measureable and tangible:
There are interesting alternatives to simple slot covers if you find yourself in a thermal quandary. With the help of a slot cooler, heat build-up can be minimized somewhat, even after you've already constructed your system.