Hi, been trying to solve this problem for a while and finally thought I'd post to see if anyone knows the answer.  
I've running Vista 32bit and have a Nvidia 8800GTS card which, when playing fairly recent games, starts hitting just over 60C.  When this happens I get a temperature warning in the form of a few beeps from my tower.  Its either 3 or 4 beeps, can't remember just at the moment  I've seen on other forums that the card should be able to handle much higher temperatures without damage so I don't really need this warning this low.  
 
Can't find an option to change temperature threshold anywhere in the Nvidia control panel or in the Nvidia performance tool addon to it.  However I'm not sure if it is the card warning me either.  I have an Atrix 9001 case with an lcd display on the front where I'm reading the temperatures, if I press one of the buttons on this screen the warning stops so it might be something to do with the settings of that screen.  Can't find any way to configure that either though.  
 
If anyone knows which it is or how to change the warning threshold please help me.  Not really a major problem I don't think just been annoying me for ages.
 

The card should and will not alarm that low, try to remove the sensor from the lcd temp/fan control unit that is on the video card and see if ti goes away.
 
The LCD may think 60 is too high, so either unplug that one or just put the sensor somewhere else you would like to monitor temps(chipset maybe ).

You can change those warning's in BIOS I'm pretty sure. I'm also pretty sure that 60ºC is one of the thresholds. You should be able to change it to 100ºC or something, or just turn it off. Chances are those arent from your card, though. I didn't know GFX cards have alarms on them.

If I remember correctly, isn't the temperature warning for 8800gts continuous? Cpu/motherboard temperature warning is in separate beeps, so maybe it's not actually from the card?

Thanks for the help, found a little 2 pronged thing and pulled it out, temperature now says 37 and I've not had any beeping  today so far despite playing a game for the last 2 hours.

so its the lcd fan control / temp mon.
 
You should be able to place that sensor somewhere else.