My assumption here is that you're already familiar with photography and you know how the aperture, shutter speed, ISO, and white balance affect the final image. If not, please read some introduction to digital photography books to get a better understanding and appreciation of how the camera settings work to get the desired final image.
I think that I've figured out the exposures to use to capture certain moods that I want to convey. Listed below are my typical camera settings. Note that these are just guidelines and not rules on how to get proper exposure in a nightclub environment.
Mode: M (Manual)
I shoot 100% on manual mode.
Aperture: f/3.2 to f/5.6
I usually shoot at f/3.2 for individuals and up to f/5.6 for large groups.
Shutter Speed: varies (usually somewhere between 1/2 - 1/40 sec)
It depends on the room I'm in and what mood I'm trying to capture.
Play around with the aperture and shutter speed settings till you get the results that you like.
Changing the aperture will adjust the flash output on the foreground subject. Changing the shutter speed will let more or less background show in the shot. (Popular Photography, June 2011 issue, p.61).
You only really have to worry about noise if you don't get a good exposure. My pictures don't have much noise since I'm getting pretty good consistent exposure. If your pictures are underexposed and you try to fix them later in Photoshop, you'll find that's when you get a lot of noise.
White Balance: Flash
Nightclubs are typically pretty dark so your external flash unit would probably be the main light source. Having the white balance set to flash would get you accurate colors so that you don't have to spend a lot of time doing color corrections during the post processing.
Quality: L jpeg
I don't want to get into the RAW vs. JPEG debate, but I've always shot nightclub photography in jpeg. I get pretty good exposures and accurate colors so I hardly do any post processing. Shooting in RAW would just slow me down. I usually need to have the photos edited and uploaded the following day.
Color Temp: 5200K
I believe that this was the default when I got my camera and I never changed it.
Color Space: sRGB
I use sRGB since my photos are just going to be displayed on the web. My photos are edited and optimized for web viewing.
Picture Style Parameters:
Color Tone: 0
I set my parameters to lessen the post processing. I pretty much get good results straight from the camera.
External Flash Unit: TTL
I don't use any flash exposure compensation. You might want to try rear/2nd curtain sync if your flash/camera body is capable of doing it. The results you'd get would be a bit different from 1st curtain sync.
The flash is bounced off the ceiling or wall at various angles when I'm shooting with the flash on the camera.
The flash is held with my left hand and positioned it at different angles when I'm shooting with the flash off the camera. The flash is pointed directly at the subject and not bounced off the ceiling or wall.