I shoot pub gigs fairly often.
I tend to shoot in manual mode, and tend to chimp to get my exposure right. If the venue has lighting you will have a well lit person with a dark background. Generally a technically correct exposure will blow out the performer and turn the background gray. Once you get to know a venue you will often have a starting point. You might then have to make minor adjustments depending on how well lit a particular performer is. Make sure you keep the shutter speed above about 1/60th, other wise you'll get blury images, this will depend slightly on your skill and also the performer. You will probably need to go faster for a SKA band who bounce around a lot but will might be able to go down to 1/30th for a blues singer. If use a 17-50 and a 35. If you're using longer lenses you'll need faster shutter times.
I also shoot RAW, it gives me much more scope to process images. I also find coloured lighting causes issues with white balance. Sometimes you'll want to embrace the colour and sometimes you'll want to neutralise it. So RAW and then adjusting the whitebalance later is the way to go.
I virtually never use flash. If I do it's often to get a shot of an audience member or a particular band member who likes to hide in the shadows (usually the bassist). If you shoot through the entire gig using a flash the band will hate you, you'll also end up with really dull looking pictures.
Make sure you set your ISO manually (other wise it's pointless using manual exposure) and make sure you know what is the highest ISO your camera produces usable results with.
If the venue has no lighting don't be afraid to leave the camera in the bag. Don't promise shots unless you know you can deliver something of a reasonable quality. Some times there simply isn't enough light, that's the way it goes.
Lens wise I used a 35mm f1.8 and a 17-50 f2.8. A nice fast lens will make you life easier.
EDIT:
http://www.flickr.com/photos/itsned/