By the coast, Pizza Port (Solana Beach, Ocean Beach, Carlsbad) are good choices and always have great guest taps and brew made on the premises.
Blind Lady Ale House and True North are good choices around the North Park area of downtown.
In the North County, Stone Brewery in Escondido and Urge in Rancho Bernardo ahve pretty extensive tap lists.
Others will surely chine in but that should get you started. We have great bottle shops so you can likely pick up some bottles to take home, too. Have fun!