Not in Seattle, but worth mentioning I think because of it's proximity...my favorite up here in South Snohomish County is Ellersick Brewery in Lynnwood, Cheers!
+1 to Old Town - a great place both from a selection and atmosphere perspective
Surprised I haven't see the Barking Dog in Ballard mentioned either - good food and awesome beer
Fred's Riverside Alehouse in Snohomish is a nice drive to a small Victorian dowtown if you want a drive. I believe they are (or were) owned by the same folks who own Bottleworks and Brouwers. Great beer and Scotch selections!
The Pub at Pipers Creek (105th & Greenwood) always has an interesting selection of beers and is just a friendly place to hang out. Eclectic jukebox, too. Oh, and two for one burgers every Monday night.