Is that your motherboard? Measure how long the card can be. There are alot of 9 inch cards now, but some GF8800 models are only 8.5 inches (inside the case). GF8600's can be very short, but obviously don't perform nearly the same. They may be a better match for your short installation location, your cpu, and your power supply.
Also, if you don't plug in the 6-pin PCI-e power connector you can get a long beep too. Did you plug a PCI-e power
cable into the 8800GTS?
What to replace depends on the system specs. What CPU you running? 2.8GHz? 3.4GHz?