It really depends on the club, the area, your band's erm... stature, etc. I'm pretty young and haven't been 'pro' yet, but even with that I've probably played in just about any payment configuration you can come up with. If you can imagine it, some club is probably doing it, or at least willing to. I particularly liked the small fee + % of the ring at the end of the night gig my old band was doing, but the place was tiny and had no natural draw and in the owner's own words: "no regulars." Particularly a good'n if you've got a lot of hard-drinking fans.
If nothing else, I absolutely abhor multi-band bills with cover charge that is supposed to go directly to the band. Even reputable clubs are good at not keeping great track, and there's so much room to screw with you. Basically, whenever there's any chance the pay changes from when you load in to when you leave, it's often a ticket to trouble. One tip is, if you can find somebody to do it, have a buddy chill by the door, keep track as well, and feed the band name to anybody who might not know it, including random walk-bys.
On the flip side, of course, you've gotta take what you can get, and if you have a big draw, even if it's just because you've got a shitload of alcoholic friends, it's a great way to make a nice chunk of scratch without being too established and get the club to love you heh.
One of the other issues though is the area you're in. I don't know, of course, but it seems pretty hard to break into the scene around Chicago without putting up with that "Three bands, $5 a head, first $400 goes to the sound guy, if you don't draw 85,000 people we don't pay you and never ask you back" crap for at least a bit, since so many clubs are realizing how much of a goldmine that setup is, and how many random bands out there just, above all else, want to play.
I don't really know what the point of this reply is, other than to say clubs and bars do everything, and you gotta be careful/watch your back. I've had pretty good luck whenever dealing more or less directly with the club/bar: when you're dealing with some sort of external 'booking agent' or whatever they happen to call themselves, it seems to pretty much be a crapshoot. Some great, some terrible.