My favorites are Breakside, Deschutes, Hair of the Dog, and Hopworks. The Commons and Upright are good for unique Belgian styles. Cascade is also a good spot for sour beers. I also like Migration and Bridgeport for happy hour, though neither will blow you away with their beer (good, not great).
Places I would skip: anywhere owned by Rogue, Alameda, Tug Boat, Baerlic, Base Camp, Occidental, Kell's (obviously).
10 Barrel got bought out by Anheuser-Busch, but the beer is still excellent and food is good. McMenamin's has crappy beer, but they are fun places to watch movies or play pool.