If you have an older G80-based 8800GTS, your card runs hot and you will need to add case exhaust ventilation below the card, and an additional input fan to provide supply air for balance. I know, I had a well-balanced, cool running system with a G92 based 8800GT and all kinds of overheat problems when I upgraded it to a G80 8800 Ultra. Adding two low case fans, a 120mm in and one 80mm out, fixed the issue.
Please describe your case type and current ventilation (# fans, size, hi or lo speed, position, in or out). Are airflow paths clear or blocked by IDE cables?
Upgrading to a cooler graphics card is a more expensive possibility, you could get an ATi 5770 and improve performance and drop heat.
If you have a G92 based 8800GTS, you may need more case ventilation, but there is some other problem. Are you running Folding@home or SETI@home software on your GPU? What is the ambient room temperature?
If not, your card already has dramatically lower power consumption in 2D mode (Windows desktop, most s/w applications). In that case your card is not making much heat, it is hot because of its environment. If the GPU fan is running high in 2D mode then either the card's fan profile is wrong, which you can adjust with RivaTuner, or your system just runs hot. You can change your fan profile with RivaTuner, but running the fan slower may sound cooler but won't do anything for the case.
You can underclock your GPU with RivaTuner, which will lower power consumption a bit, but won't make much difference in 2D mode as it is already rather low.
Unless you have some background software forcing the card into high power consumption mode, it sounds like you have a case ventilation problem, perhaps complicated by high ambient temperatures.