No, they do *not* use a standard 3-pin connector. They use a 4-pin connector that is *not* compatible with PC 4-pin PWM fans. They do not work in the same way as PC fans - i.e. they vary their speeds depending on a different voltage source compared to PC fans so you can't build yourself an adapter unless you forcibly limit the voltage and limit the fan speeds (not recommended). While on paper the fans may be similar to other fans (i.e. the power cables use 5v, 12v, ground and signal lines, their speed is varied by the logic board changing the 12v power line rather than the 5v power line which most PC fans use (it may be the other way around though, I forget). I can guarantee you that they are not PC-compatible in terms of connector ends or even after being rewired. I know they can be jerry rigged to run off PCs using a hacked molex adapter and I believe a resistor to bring down the voltage manually, all fan speed control in such a situation is lost.
There are no compatible newer fans for the Mac Pro unless Apple have sourced even quieter fans in the 2009 Mac Pros, in which case those *may* work but good luck finding them.
To be honest, Apple's fans are about as quiet as they come. I've compared them to some of the quietest 120mm PC fans available (Scythe Kama PWMs) and the Mac Pros are quieter.
If you're desperate to use quieter fans then you could, in theory, get some 3 pin ultra quiet fans and run them through fan speed adjusters connected to the molex cables in your optical bay. You'll end up with a pretty nasty mess of cables though and chances are it won't be quieter than the Mac Pro's existing fans. You'd also run the risk of overheating since the fans would be stuck at a constant speed and couldn't be sped up if the CPU is overheating under a heavy load. Your machine would also then at least fail the Apple Hardware test although I think it would run ok in OS X although your log file might register some sensor/fan failures due to the lack of detectable fans.