a few more to check out:

* velo bike shop, on capitol hill: http://velobikeshop.com - my LBS! small store, mostly bianchi bikes, very knowledgeable staff. lloyd, the owner, is a really nice guy, and knows a lot about all kinds of bikes. they do wheel builds too. (granted, you might have to buy something big before they get really nice towards you, but that's the same everywhere i guess)

* 20/20 cycles: down on union street somewhere, i think they cater to the fixie/mess crowd

* counterbalance - lower queen anne area, they have road bikes & fixed gear bikes.

* il vecchio bikes - http://www.ilvecchio.com/ - more of a boutique kinda place i think, but i want to check it out some time

* (eastside) Sammamish VAlley Cycles is a good place, especially if you do any randonneurring rides. ~20 miles east of seattle, but worth the trip.

and an exhaustive list from google.

lucky for us there are so many good shops around here!