Living in Olympia, I routinely hit all the Portland LFS about every 2-3 weeks. Sorry I didn't catch this thread earlier.
Waves either moved or went out of business, and is no longer on Lower Boones Ferry. Too bad. However, Hollywood Aquarium just relocated to right around the corner from the old Waves location, nice big place and nice people (Shaun from Waves works there now). Unusual macroalgae from Jakarta, and a great stock of tanks and oak too. Take Durham exit 291 and go left just a mile, then cut right into business park area and wrap around to the left less than a mile. Be sure to check out the Wild Oats Market grocery store at that right turn, very unusual and they have lots of free samples on Saturday. One day they even had a beautiful model serving wine samples in glass wine glasses (she wore a fuzzy pink bunny suit complete with ears to make it clear they are not wine snobs.....)
Upscales is very good, but don't seem to know what they are doing if you really quiz them. One guy knows his stuff though. They get very unusual showy orange Gorgonia's, plus their display tank has the largest clam I have ever seen. Dry goods are way overpriced but again, interesting stuff. Take the Tualatin exit one down from the Durham exit, go to the right, BUT STAY IN THE RIGHT LANE or else you are in a world of hurt with no turn around. Of course, continue down I-5 just a couple more miles to Fry's Electronics in Wilsonville for the largest DVD selection I have ever seen, plus tax free shopping.
Soutas is a good place if you deal with the owner Rick, a nice guy. His hired help seems a bit lazy, not even wanting to lift up and show me the live rock when I recently bought $465 worth a while back. Great rock and prices on it though. I don't trust the help's price quotes on corals either, I think he tries to pocket some extra on the weekends. Don't forget Woody at Seahorse Supply right off of MLK Way on Russet St, small but interesting shop with many years of experience and sincere advice.
I always make an expedition of it all, with other stops at the Laurelwood Brewhouse in Hollywood, the Raccoon Lodge brewpub on Hwy 10, and the Alameda Brewhouse north of Hollywood, all fine places. Ridgefield National Wildlife Refuge at I-5 milepost 16 or so in WA is worth a short side trip with an 8-10 mile nice gravel drive through wetlands and stunning bird watching. Go left to the River S unit, gates close at dark though.