I like the Beachcomber in Mission Beach on Thursday nights, it's a shithole but the drinks are cheap and there are generally a good amount of hot girls there.
Typhoon Saloon in PB on Fridays/Saturdays or Wednesdays (wednesdays has a hair metal cover band, this is the busiest night of the week and it is packed, if you dress 80's hair-metal you get in for free vs. 5-7$).
Downtown I like the Sidebar for Fri/Sat, also the W (get there early). Both are a little more classy. There's a cheap parking garage on the corner of 6th and market. Stingaree is supposed to be cool, but I haven't tried that out -- very bling bling pimped out atmosphere.
Try to be in the bars prior to 10pm unless you have connections, some places even earlier is better. My record wait is 3hrs and 45 minutes outside the W. The W is the worst wait of any place. They card in San Diego like a motherfucker so don't try and pull fake ID shit, especially in Pacific Beach unless you want your card jacked.
Hit the beach at PB drive if the weather is nice, also mimosa's at World Famous at PB drive (hot waitresses here). And finally, for huge and fantastic breakfasts hit up Hash House A Go Go in Hillcrest. Have fun, SD is the shit.