I've done this road trip twice (well, three times if you count back-and-forth on one trip) for a combination of camping, fishing, and beer touring. We stopped at literally dozens of places! My top recommendation is Rouge in Oregon. Great beer, good food, awesome vibe, and beautiful scenery. The second is Lagunitas, about an hour north of San Fran. The beer is great, the food is good, and the vibe is welcoming with local bands playing many days. Kinda a crappy location in that there's not much else to do, but it's a good stop on your way.
Those were my top two. Here are thoughts on other popular ones.
Though touristy, the McCallister Breweries in Portland can be fun. One is in an old high school, so you can drink in bars that used to be classrooms or check out the gym and swimming pool. OK beer, so-so food, but nifty buildings.
I agree with another poster about Anchor Brewery in San Fran. Good stuff!
I was disappointed by Russian River. The food was bad, the beer wasn't different than we get in San Diego (but we're a beer paradise, so Russian River beers make it here often). The town is expensive, too.
Eureka, CA has several breweries such as North Coast. Though all good, the experiences didn't make me call them "destination breweries" like Rouge or Lagunitas.