Serious Eats - seriouseats.com

NEVER AGAIN:
I have been to Casellula several times over the past year, but I will NEVER GO AGAIN after I finally realized that the service is unforgivably terrible. I have always enjoyed the food and wine selections but I can no longer overlook how rude and inconsiderate the staff is (which has not changed in several years despite many negative reviews and complaints on the internet!). When one pays a 300-400% markup for wine and $14 for four spoonfuls of macaroni and cheese, one should expect at a minimum courteous service! Do not be fooled by other reviews that simply focus on the wine and food—you will regret you ever stepped foot inside Casellula (unless, of course, you enjoy being treated like an annoyance).

I highly recommend the Mexican food at Guaymas in Tiburon.

May I suggest in Seattle...(in no particular order)

Bakeries / Sweets:

Top Pot Doughnuts
Macrina Bakery
Sugar Rush Bakery
Trophy Cupcakes
Hiroki
North Hill Bakery
Sugar Bakery + Cafe

Not just bakeries:

Kingfish Cafe (soul food / killer red velvet cake)
Roti (Indian food)
Lunchbox Laboratory (craziness as detailed above by another user)
Bimbo's Bitchin' Burrito Kitchen

I second the Cheeseboard in Berkeley... it really is amazing. And if you're in Berkeley, then I also suggest Brazil Cafe. As for SF, skip House of Nanking. As mentioned above, many of the sauces used taste the same.

cheeseboards for sure and north berkeley's gourmet ghetto is a great place to explore for good food.

If you're right by Pike Place, I second El Puerco Lloron on the Pike Place steps. The machaca is fabulous and you can watch them make the fresh tortillas. I am very bummed to have just found out that my other favorite place closed over a year ago. :( Guess that's what I get for moving away. :( Ivars at any location is good! LOVE the clam chowder. And if you ask "which kind?" don't bother going. :) Oh, and if you want really good coffee (and some mighty tasty baked goods) Cafe Vivace off Broadway is great and a nice break from the worldwide hometown brew. Vivace has another location I haven't tried, and speaking of S-bucks, the original flagship store is right there at Pike Place, too. :) I watched Spoon-man perform right outside there. :)

No one has mentioned it yet, but Ten-01(which is right across from Powells) has a "power lunch" for $15. A first course, a second course and then a tray of asst' cookies, truffles, and gelees. A real bargain at in a beautiful space.

Pok Pok is also affordable and somewhat unique.

And, there are tons of happy hours here that offer excellent food, including Ten-01 and Clyde Common(also near Powells), which, I think I would normally put in the "pricey" category if I was an intern.

Biwa and Tanuki are also extremely affordable, japanese, izakaya style restaurants(although the owner of Tanuki considers it a bar. But excellent food).

I also recommend Sahagun chocolates if you're around Wed-Sunday in Portland. Excellent hot chocolate, great chocolates plus homemade sodas and ice creams.

Have a great trip.

I should've known how hard this would make everything be... now I have to sit down and make some SERIOUS decisions. Luckily I am traveling with a friend with an appetite. We'll be eating little bites from as many places mentioned as possible!

In Seattle, we're staying at the Green Tortoise right across the street from Pike Place Market–looks like I'll be spending at least a good day in there.

Hopworks is great in portland for an amazing ipa, and the best soft pretzel sticks... ever. I haven't tried the rest of the food, but im sure it's good. The enviroment is really cool too. I recommend
Andina in the peral is awesome Peruvian food, it's a bit expensive though.
Esparza's has amazing texmex in se portland. great tamales and mole.
For cheaper lunch food, Laughing Planet on 21st and also on Hawthorne is a favorite of mine-- lots of veggie stuff and interesting burrito combos.
Pok Pok is always popular.... you should probably go there too.
Ah, I miss portland already..

Just got back from San Francisco, and had great food at Chiaroscuro, Destino, Frascati, and Regalito (in the financial district, the Castro, Russian Hill, and the Mission, respectively).
None are incredibly cheap (my boyfriend and I alternated between eating granola bars and eating at restaurants), but none are outrageous.
There is also a place called The Little Chihuahua on Divisadero Street, which is quite decently priced, and quite good.

Links (their descriptions are better than mine would be):
http://www.chiaroscurosf.com
http://www.destinosf.com
http://www.frascatisf.com
http://www.regalitosf.com
http://www.thelittlechihuahua.com

Highest on my list are the sandwiches served at lunchtime at Chiaroscuro, and the bread pudding at Frascati. And a baby burrito at Little Chihuahua will stave off hunger for many many hours :)

You may also want to try the baked goods at Miette (in the Ferry Building and another location which I cannot remember).

I agree with emilydev that Fire on the Mountain in Portland is the best place for wings, microbrews and fun. Their "soon to be famous peanut sauce" is addictive! And everything else is good too. Ever have a fried twinkie- if not go and enjoy one. You won't be sorry. The Burnside location is bigger and newer.

Higgins is my favorite spendy restaurant in Portland, but this is the best town for cheap eats! Toro Bravo has AMAZING (and well priced) tapas, and you shouldn't miss a local brew pub (Lucky Lab is very Portland.) Stumptown Coffee is great for a pick-me-up and the Stumptown Annex (on Belmont) has daily cuppings. My favorite hidden gem is a total pit of a taco shack on SE 82nd near Woodstock called Urapan- the best salsas and tacos al pastor I've ever had. Have fun!

I say skip House of Nanking -- somewhat touristy and all the sauces taste the same (probably because they use only one mother sauce). Instead, head out to San Tung in the Inner Sunset. Their dry fried chicken is legendary (order diced!).