Mister B's - more for the jazz and blues purist. Tiny little place and you'd better not chat when someone is playing or you'll piss off the regulars.
Jazzbar Vogler - I love this place. Top quality acts, top quality drinks and top quality service. No complaints... none.
Jazz Club Unterfahrt - haven't been there in quite some time but had good fun there. Fairly spacious cavern-type place with regular jazz and blues jam sessions. Nice to see musicians just showing up and joining in.
Waldwirstschaft - beer garden, also known as WaWi, usually has live music. Unlike most beer gardens, where it's oompahpah band brass music, this place has mostly swing type jazz and blues. Beer garden is frequented by the swanky crowd, just check the carpark on your way in.
Long Night of Music - Every year, first weekend in May, Munich hosts this event with 4 bus tours taking you to approx. 100 live music destinations around Munich all night long. All kinds of music will be represented including, of course, Blues. The website of full info is here: http://www.muenchner.de/musiknacht/
Hide Out - has great live blues with an open jam session on Thursday nights. Located in Rotkreuzplatz (look for the small white neon sign next to Tschibo) is probably the best blues and rock club in Munich. Unknown local acts perform as well as known touring acts from the US and Britain (Chris Jagger, etc). Six nights a week! Start your evening directly across the road in Muffins & More, a licenced latenight bakery that also plays blues and sells blues CDs. Great bagels, fabulous cheesecakes too.
Piazza Linda - Owned by New York Entertainer-Singer, Linda Jo Rizzo, Piazza Linda brings back to life a small live stage like Munich used to be in the 70's, along with southern italien recipes from her father's kitchen. On the live music nights you will find music for all tastes from jazz standards & classic, thru to soul & blues, latin & modern.
Café Beethoven - live Blues music sometimes.
Further Info - And for more about the Blues scene in Munich - check Peter Krause's website: jazzinstitut.de (all in German, of course)