Portland native here... Lots of creators and publishers here which turns into a bunch of shops.
Here's the breakdown for Portland and Vancouver:
I Like Comics - Vancouver - New issues, graphic novels, and a REALLY deep selection of vintage and keys. Also bagged sets of complete runs. You want an X-Men #1? Brave and the Bold 28? Go here.
Portland:
Cosmic Monkey - New Issues, graphic novels, decent selection of non-key back issues. Has 3 or 4 boxes of rare/collectible books under the front counter, but you have to know they're there and ask for access. Parking sucks because of the coffee shop next door. Currently my preffered shop.
Excalibur - Probably the best selection in town. New Issues, graphic novels, deep selection of non-key back issues. Rare/Key issues on the wall and under glass, not as rare or key as I Like Comics. Parking sucks because of the weed shop next door. Comics are all sealed, no browsing.
~~Cloud 9~~ Now Tastee Cat Comics - Not far from Excalibur. Smaller selection of, well, everything, but they come through in a pinch because nobody knows they're there. Parking should be just as bad as the others, and yet it never is for some weird reason.
Future Dreams - Used to be my preferred shop then they lost their lease a few times and kept moving. Now they are in this weird basement space that's entirely too small for what they have. They need a professional organizational assistant. They might have what you want, you'll never find it there. :(
Floating World - Recently moved to Lloyd Center Mall. Use the roof-top parking close to the food court, then walk East inside about a block, past the Game Stop. Specializes in mostly indie and zines. Also publishes Indies and Zines. They have mainstream current issues and graphic novels, but that's like, not their jam, man.
Comics Adventure - Haven't really been there enough times to form an opinion yet. Selection is better than Cosmic Monkey, not quite as deep as Excalibur. Has some interesting rares and keys.
Books With Pictures - Heavy on Indie press, but not as heavy as Floating World. Mostly new issues and graphic novels, no real back issue selection. Bonus - heavy LGBTQ representation if that's your deal.
Acme Comicbooks - So get this... I've been living in Portland for 30 years and never heard of this shop. Popped up one day on a Google search and I thought I'd check it out. TINY store. No current issues, no graphic novels. Bunch of bronze age back issues. The whole time the owner is going off about how long he's been in business (weird, l've never heard of him), how he has the best selection in the Northwest (seriously, I personally have more books than this shop does), and how other shops are ripping me off. I will say he does have some interesting vintage non-comics stuff... but overall, it's like a stall at an antiques mall, no theme, no selection, just randomness. Worth it for a laugh maybe?
Fall Out Comics - Got their start in an honest to god bomb shelter. Moved to a better location. Same organizational problem as Future Dreams, but more open and accessible. No current issues that I saw, all back issues starting 2 to 5 years old and back from there. Probably an outlet for those "We buy comics!" road signs.
Rose City Comics - Small shop, limited back issues, mostly current issues and small selection of graphic novels. Parking is almost impossible due to the district they are in and proximity to Blue Star Donuts.
Things From Another World - Multiple locations. Seems to focus more on merchandise these days than actual books. :( You want new issues? Fine, get ready to wade through a bunch of action figures and Funko Pops. Milwaukie store is the main HQ across from Dark Horse comics. Close to Comics Adventure.
Comic Cave PDX - It's pretty much the ideal neighborhood comic shop. Plethora of new issues, small selection of all ages, graphic novels, back issues. A few slabbed keys.
The one thing they do differently from everyone else is creator specific short boxes. Looking for Alan Moore? All in one box. Bonus: First box I saw was for P. Craig Russell and Michael Kaluta. It's a neat idea and appeals to my "alphabetical by author" bookstore training.