I like Elliott Bay Brewery for their large selection of organic beers and great food. They're West Seattle and Burien. Oh and they let me look at their beer book with ingredients, so I got to taste different IPAs and what not and then check out which hops they used.
My top 2 are Brouwer's in Fremont and The Stumbling Monk on Capitol Hill. Both have a large selection of rare beer and usually a few good sours on tap and several Belgians to choose from.
What are your favorites?
I went to Brouwer's on my first visit to the city... that place is fan-freakin'-tastic! The staff is knowledgeable (if a little less than pleasant, but I'm not there for the attitude), and the selection is great!
I'd have to agree with Brouwers and Naked City. But I'd like to give a shout out to Old Town Ale House in Ballard. It's not a huge selection, but they always have a great selection on hand. It's low key and kid friendly (a huge plus for me). They also have great food, try the Ballard beef dip.