Love Hoffers, 24 taps, new stuff on all the time. They have good accounts, so often get rare brews. Smoking patio out back, 2 humidors for cigar lovers.
In downtown La Mesa. Great staff, relaxing environment.
I have heard really great things about The Abbey in North Park. Good food and several micros in bottlesmixed with a nice staff and a great place to watch football.
Live Wire on El Cajon Blvd, just west of texas st. Everything you want in a dive bar, a great beer selection and the staff knows the beers.
Areo Club on India St, just south of washington (one way street so you have to circle around) Great beer selection and one of the best stocked full bars in San Diego.
Blind Lady Ale House, on Adams Ave. Lots of local and regional beers and fantastic craft pizza.
Jewel Box, on 16th and F. Right at the foot of rt 94 as it enters downtown. PBR on tap and surprisingly good food.
And a ton more. There is no shortage of good bars in SD.