Lake Tahoe as well if you are willing to drive off your path for a bit.
If you are a wine enthusiast, Napa Valley is a good stop.
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Northern CA: so many brew pubs. Near Eureka, if you like fried chicken, the Samoa Cookhouse. Old logging kitchen. Big trees. See the big trees!
Portland: Voodoo Donuts, Saturday Market, Food trucks, Olympic Provisions
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WOW! OK, that’s one or two suggestions there. I’m going to have to make my spreadsheet bigger (…of course I’ve got a spreadsheet!). I’ll be doing research for a while. Just wanted to say a big thanks so far folks 
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How exciting Nathan, sounds like an awesome trip! Glad you’ll be visiting our little chunk of the world. Yosemite will be the oddball location as you’ll be going 3.5 hrs out of your way just to get there and you’ll have to back-track to get back to the Bay Area and the rest of the trip. Yosemite is incredible though, so it’s worth the effort. Just give yourself enough time to get there and take it all in.
As you go north from SF and over the Golden Gate Bridge you hit an area full of quaint towns, beautiful wineries, farms and incredible artisan cheese stops. Food, wine and art is the huge attraction here. You can easily spend a day or more wandering, exploring, eating and drinking. There’s also a couple of oyster farms where you can sit outside enjoying the ocean eating fresh oysters on the half shell. (I heartily recommend Hog Island Oysters!) If that kind of wandering interest you, you should give yourself at least a full day to explore the area.
If you search “Russian River” you’ll find a lot of bed and breakfast places, pubs and other neat things. The Russian River is beautiful place! You can also take the Pacific Coast Hwy (Hwy 1) right along the cliffs of the coast and stop at all the great little small towns along the way. There’s several cool historical spots to stop and explore as well.
Depending on the time of year there are always artisan fairs, festival and other nice events going on along the PCH and wine country so it’s worth as search to see if anything going on interests you. It’s also good to know if there’s a popular event going on as you might want to avoid the area as well 
One last thing, keep in mind that the devastating CA fires have destroyed an awful lot of our wine country. So call/seach around and make sure things are still open if you are going into the effected areas.
These links might interest you. I would suggest really searching the Sunset magazine site as it’s about the best guide to activities and places on the west coast.
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There’s also this thread about things to do in Seattle:
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Stop in Ashland (southern Oregon on I-5)! Charmingly beautiful town with a robust theatre community, especially in the summer when they’re running their Shakespeare festival (which performs many non Shakespeare works as well)
In Seattle you can catch ferries to many nearby islands or even go to Victoria Island in Vancouver, Canada, where Butchart Gardens is a must see.
If your trip happens during April - a couple hours north of Seattle the entire Skagit Valley is filled with rainbows of tulips http://tulipfestival.org/.
Seattle has a huge music and arts festival every summer called Bumbershoot, dates this year are August 31-September 18.
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Here (below) is a list of things to do in Seattle that I prepared for a former coworker. Enroute if you can swing by Crater Lake, that is worth seeing. Also Mt St Helens.
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The most common tourist activities around Seattle are:
Space Needle (also nearby is the pacific science center, monorail, the experience music project, and the science fiction museum)
Pike St. Market
Seattle Underground Tour
Boeing Plant Tour (IIRC - this one is close to Bothell)
Woodland Park Zoo
Museum of Flight
If you have a day available, some great outdoor places are:
Mount Rainier - There are many great hikes and things to do there. It takes about an hour and a half to drive there from Seattle.
http://www.nps.gov/mora/index.htm
(Note: check conditions - when I sent this to Steve it was in the summer - they may already have some snow there and possibly roads closed)
Olympic Peninsula - This is a big place, with many things to see - way too many for one day, and it does take a while to get there. We usually take our car on the Ferry to get there, which is fun in and of itself. If you do one thing on the Olympic Peninsula, I would recommend Hurricane Ridge:
(same warning about checking conditions)
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I did the same trip. Avenue of the Giants and Fern Canyon were highlights.
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