I really like
Fat Tire Farm, a primarily mountain biking store in Portland. I bought a brand new Kona Dawg Primo there about 2 weeks ago (so fun!). They're prices are pretty much straight up MSRP, but they have a great selection, are reasonably knowledgible, and friendly.
River City Bicycles also has a wide selection of both road and mountain bikes. They have something of a faint yuppie vibe that turns me away a little bit, but I honestly can't say anything negative about them from the shopping I've done there.
Plus there's several Performance Bike stores in the Portland area for the price-minded. They have better deals and usually very high stock, but not as much choice for higher end rides.