Gotta agree on the stop at Blake Island, always worth the walk around the island for stretching the legs and enjoyable scenery.
Also reccommend Bell Harbor in Seattle. The walk north on Alaskan is short to Broad Street, and a steep walk up Broad to the Seattle Center and the Space Needle for some panoramas. EMP is also worth a gander and some interesting architectural shots. Pike Place Market, Seatttle Art Museum, Westlake Park, 5th Ave, Pioneer Square, China Town and the new Great Wheel at Pier 57 are all options and not to far of a walk.
The Museum of Glass in Tacoma is up the Foss waterway, built a new public marina next to the museum in '02/'03.From what Tacoma waterfront used to look like 15 years ago, the improvements and environmental cleanups, make it much more pleasing then it once was.
If you are going down to Tacoma, should plan for a day or two in South Sound. They have many State Marine parks to choose from, much more then center and north sound. Leaving south sound, go up Colvos Passage for favorable current, Quartermaster Harbor on Vashon Island is always worth a stop as well as Gig Harbor and the beginning of Colvos. Stop at the Tides In for a micro-brew, hamburger and fries. The public dock in Gig Harbor and Harbor History Museum is worth a gander and check out T-Bird #1.
On up Colvos you come out at Blake Island, if you missed it on the way down, make a point of stopping by on the return trip. Rather then head up sound, I recommend going on the west side of Bainbridge Island via Rich Passage (check your tides and come in on a favorable current). If you wish you can check Sinclair inlet and Port Washington Narrows,many varieties of waterfowl and birds, if you've got a 400 to 600mm telephoto.
Heading up Port Orchard Channel always worth a stop in Brownsville for a sandwich and soup, and the sailors and locals here are usually very warm and friendly. Heading on north to Poulsbo is always worthwhile, if not for the fireworks at least check out Poulsbo Bakery. Once again check for favorable tides leaving Liberty Bay and around Pt. Bolin to Agate Pass, usually you'll gain about a knot average overall all the way to Kingston.
I recommend keep steaming or sailing North to Port Ludlow, unless you need to stop for fuel in Kingston (there are eateries in Kingston as well). Leaving Port Ludlow if you wanted another interest side tour, head down Hood Canal and spent an evening in Pleasant Harbor and enjoy a swim, hot tub or golf. (check your tides again)
Heading on north if you haven't stopped by Port Townsend, do so now and take time to walk the whole town, even walking down to Boat Haven isn't that far and worth a stretch. Stop at Pennysaver for the coldest beer and very large selection of sandwiches, or stop at one of the many sit down eateries in downtown PT. The new Marine Center and surrounding neighborhood marine establishments is usually an interesting walk, as well as downtown PT. If you really want to stretch your legs, going uptown is worth it for the architectural eye candy and stop at the old/new general store for an ice cream or up the street for movie.
Usually it's preferable to leave Port Townsend on the morning ebb in the summer, for a quick boost out the Straits and catch the flood back into San Juan Channel at Cattle Pass.
Seattle Waterfront before the Great Wheel from Belltown Harbor