Chucks (both Central District & 85th) Beer Junction in West Seattle Malt & Vine in Redmond 99 Bottles in Federal Way Full Throttle Bottles in Georgetown Beer Authority in 522 And nearly all Metropolitan Markets & Whole Foods have a great selection of craft.
I am amazed sometimes at the beers that show up at Ballard Market. They had like 30 bottles of Logsdon P&B on the shelves a few weeks back.
Really depends on what neighborhood you're in and what you're looking for. Some places (like Bottleworks) seem to sell out almost instantly on a lot of the limited releases, whereas other spots like Beer Junction and Chuck's seem to hold them a little longer. Beer Authority up on Lake City Way also doesn't get much mention on here. Whole Foods Roosevelt, U Village QFC, Metropolitan Market, and Central Market Shoreline (as well as Ballard Market, already mentioned) all have strong selections considering they are grocery stores.