The Boondocks regularly books bands, mostly of the louder sort. Cushing St., having recently re-opened, I don't know their full plan, but they've welcomed the twice-monthly Irish session, and another time I was in there they had a jazz (or something??) band. Montgomery's also books a variety of performers (or at least there are two groups I know of -- one Irish trad, the other the Mollys). O'Malley's I think mostly has rock and loud stuff (I'm speaking from my biases, though, and assuming you're a solo singer type). Stein and Dine has new management -- that's where the Irish session moved from -- so I don't know what they're up to lately. Other possibilities I can think of are Plush (have a variety of music), Hazy Dayz (have a regular songwriters' series), Epic Cafe, and the Bookman's bookstores (an AZ used books chain).(I frequently find myself trying to answer this question and I'm really the wrong person to do it, being a hard-core traddie who doesn't get out much. However, since my name's out in the world in assocation with TFTM, I'm often contacted, and try to be helpful... You could PM me a mailing address, and I could send you the "Night Life" page from the Friday paper!)
I imagine there's a lot of competition for gigs around the Folk Festival. Good luck in your search!
~ Becky