If you decide to visit the EMP make sure you also visit the Science fiction museum which is downstairs from the EMP. I enjoyed it at least as much as the EMP.
IIRC you can buy a ticket for the EMP, SFM and the Space Needle for one price and save a couple of bucks.
If you are into trivia check out this thread and meet some Seattle dopers. Good group. I have done the trivia night a few times, and made money on the deal once or twice. 
Truth to tell, I didn’t love Seattle the way I thought I would. I will, however, return to see the Museum of Flight, the Boeing tour and I might try the San Juan Islands day tour. I did have fun on the Duck tour and I ate very well in the area around the Pike Place Market
If you’re interested in some easy walkabouts en route to Seattle, I would recommend the Columbia River Gorge , which you can get to by taking I-84 out of Portland to the east. Multnomah Falls is gorgeous, and there are a lot of other easily accessible nice spots along the historic drive. You can pick up I-84 by taking the I-205 around the east side of Portland, but I’d have to ask a PortDoper’s opinion regarding whether that’s really any quicker.
There’s also Mt St Helens, but that’s even further out of the way.
Going alone? Like to read? Try the Coast Starlight Express, a train. Expect a couple hours of delays beyond the scheduled times.
Pike Place mkt. Great grazing there too- slice here, crab cocktail there, ect.
Underground Seattle tour.
Crater Lake is worth a visit. I’ve made a side trip there while driving from Seattle to San Jose in two days.
Two essential things to do in Seattle IMO:
Pike Place market + the waterfront parks.
Ferry ride into the San Juan Islands.
Both of these are substantially enhanced by nice weather, which as you may have heard is a relative rarity in those parts…I still miss Seattle a ton though… 
I’d second the suggestion to take the costal highway if you’ve got the time, it’s a lovely drive. I-5 is pretty visually boring with the exception of the mountainous bit crossing the Oregon border. It’s much faster, though. Also, if you take the I-5, definitely follow instructions re: gassing up and the Ashland/Medford exits.
Personally, I’d love a train trip except I can never figure out why it’s both hideously expensive and excruciatingly slow.
Thanks for all the help- And I think I’ll definitely join a Pub Quiz if there’s one while I’m there. (Come to think of it, Yelp does a lot of Pub Quizzes in Seattle, too.)
I’ve decided I’m driving, at this point. Honestly, for me, “driving vs flying” ends up being “anyone have a good reason I should fly yet?” And the answer is always no. 
Thanks for all the suggestions, though!
For those of you keeping track, I’m keeping a running tally of stuff I expect to do here.
If you are really a beer dweeb, a stopover in Portland may be worthwhile.
The Seattle Underground Tour is a hoot-- keep it on the itinerary.
If you want to buy bottled beer, head to Bottleworks in Seattle-- very good selection, including some more obscure Belgians.
(Bump)
Anyone know anything about the Architecture Tours? There’ll be an Art Deco tour while I’m, there, and while that sounds great, I don’t like making commitments on vacation. Do these generally sell out, or will I be able to stumble down there at 10am and get in on it?
My WAG is that the tours won’t sell out. I don’t think they’re very well known here, and one doesn’t exactly see huge group of architecture-tourists stumbling around downtown (though there’s plenty to see). I was in Chicago recently – now there’s a city with some architecture tours – and easily found a spot in the tour I wanted without a reservation. Seattle’s probably even easier.
Is there anything to do at Microsoft or Nintendo HQ? I wouldn’t mind visiting their corporate museums or whatever they might have along those lines. Anything there besides office parks?
Microsoft has an interesting, albeit small, museum (though I think I saw it circa 1997, it may well be a vast display by now…).