Oh Man- don't get me started.
Near my house (south county, Miramar area) there are a bunch of MUST VISIT breweries:
Green Flash
Alesmith
Hess (reppin' the nanos)
Ballast Point Old Grove location
Karl Strauss Brewery Gardens (nice spot for a family dinner)
Also nearby is Wet 'n Reckless (wouldn't recommend, but a personable proprietor) and Rough Draft (forgettable, too fancy for my taste haha)
Stone is a Must-See as well, honestly if you're going to be in North County and can only see one brewery, go to Stone. Awesome food, good tour, great grounds, neat building, epic beer selection. Make an afternoon of it.
Also in North County there's Lost Abbey/Port Brewing, a great brewpub called the Breakwater in Oceanside, a few nanos like On the Tracks and Mother Earth.
Others to check out if you're near them (doesn't sound like you know where you'll be yet):
Alpine, Automatic, Amplified.
Those are just my favorites- there's about a billion more. Got to give 1st priority to my SoCo homeboys (and girls) because I think they're doing the best work in the county right now and a little underappreciated.