These are some of the cooler, smaller new & used record stores in this area that also have websites or online sales. The intensity of their Web involvement varies, but if there's something you didn't find on my Garage Sale site (like a rare single or CD by a Seattle band, for instance), these websites should help... or just call 'em and ask.
Sonic Boom Records Lots of indy new'n'used CDs, LPs, singles. (Seattle, WA)
Easy Street records CDs and tons of vinyl. (Seattle, WA)
Singles Going Steady Garage, punk, ska, indy, hardcore stuff. (Seattle, WA)
Second Time Around Used'n'indy store with a 30-year history. (Seattle, WA)
Jive Time Records CDs and tons of collectible vinyl. (Seattle)
Earth River Records CDs and tons of vinyl. (Seattle, WA)
Repeat the Beat New'n'used, CDs and vinyl.(Seattle, WA)
M&L Collectibles Tons of collectible vinyl. (Seattle, WA)
Rockboss.com An online co-op store for several Seattle indy labels
Rocket Records (Tacoma, WA)
The Business, and Knw-Yr-Own Records Indy and collectible/used CDs/vinyl. (Anacortes, WA)
4000 Holes (Spokane, WA)
House Of Records (Eugene, OR)
Django's Big selection of new and used CDs. (Portland, OR and Seattle, WA)
Crossroads Music (Portand, OR)
Music Millenium (Portand, OR)
Sonic Recollections (Portand, OR)
Ozone Records (Portand, OR)
Sonic Recollections (Portland, OR)
Jackpot Records (Portland, OR)
Fallout RecordsA Seattle landmark since 1984, now sadly defunct. Last time I checked the website was still up, with some very cool links and historical photos.
And here's a link to a continent-wide database of indy record stores: http://www.RecordStoreReview.com, check it out.