Take a ferry and visit one of the islands. (If you're staying downtown you can get direct ferries to Bainbridge or the peninsula, or you can drive a bit north and take a ferry to Whidbey or a bit further north and take a ferry from Anacortes to the San Juans, head south to West Seattle and take a ferry to Vashon).
Pike Place Market (and downtown shopping)
Underground Seattle
Check out the Ballard Locks and visit the Fremont Troll and all the kitschy stuff in that area.
Space Needle and Seattle Center (Chihuly Glass, etc.)
Ferry into the San Juans would be fun, but I'd take the Clipper to Victoria! It's super fun, and can get you there easily and quickly enough that even one night is worth it.
I like MsBPO's list, too. Don't miss the Underground Tour!
Everytime I see these posts I am reminded of all the stuff we haven't done considering we're Seattle natives lol.
I keep meaning to do the underground ground.
Me too.
Go to Beechers in Pike Place Market! They have awesome cheeses and some awesome mac n cheese.
Take a ferry to somewhere. If you come to Bainbridge Island make sure you stop at Mora Iced Creamery. They have awesome ice cream that they make right here on the Island.