Casey,
There have been numerous discussions on cruising in the area before. Typically in response to a "I want to cruise near Seattle" inquiry. La Connor (already mentioned) is a favorite and has been the site of previous CBGT's.
Farther south, the Port of Everett is worth a visit and is a good launching point for those looking to trailer in and cruise. It's the largest launch facility in the area with 14 ramps and plenty of trailer parking. Long term parking is available and the lot is patrolled. The marina is quite nice and sports a local brewery near the East end and several restaurants near the W end.
Around the bottom of Whidbey Island and across the way is Port Ludlow. Port Ludlow is a lovely quiet port that serves as the entrance to the Hood Canal. It has a very nice hotel if one is looking for a spot to sleep off the boat. It also has a couple of good restaurants.
Farther south in the Hood Canal is Brinnon. There's another nice, small marina there that is extremely well protected. There's a pool and a hot tub at the marina and good pizza is available there. A small store provides the basics. That's as far south down the Hood Canal as I've explored.
Back around the other side of the Kitsap Peninsula, Kingston is another great little stop. They have a nice market on Sat. AM just at the N end of the marina and there's plenty of restaurants and bars within easy walking distance.
From Kingston, you can slide SW through Agate pass and then WNW to hit the port of Poulsbo. There's a cute little science museum, a couple of galleries and several restaurants within walking distance of the marina in Poulsbo. If I recall, JJ's has good fish and chips.
Back around the east side of Bainbridge Island is Eagle Harbor. There's a ton of good restaurants and bars within walking distance of the marina and there's a good grocery store about 1 block away also. It's a good place to stock the kitchen. There's even a couple of wine bars and a winery tasting room on the main street there. Many cute shops are available on the main street also for those who like to shop.
Across the way to the east is Seattle. There are several possible marinas to stay in near Seattle but for me, Bell Harbor is the best placed. From Bell Harbor marina, you can easily get anyplace downtown. Take a cab or bus to see a ball game in the summer, explore the Pike Street market, visit a museum etc. It's all available and the local bars and restaurants are excellent.
A little to the S of Whidbey is Blake Island State Marine park, a favorite stop for many brats. There's not a ton of dock space, but there's often plenty of space in the off season.
Tillicum Village is right there. They celebrate NW Native American culture and provide good dinners during the tourist season.
Farther S and around the tip of Maury Island and then back N is Dockton county park. There's a bare bones dock available for moorage there and I recall one of my earliest CBGT's (a small one) was held there.
Even farther S is Tacoma. I haven't personally taken my boat there but I know there's moorage to be had at the marina near the Museum of Glass. That museum houses all kinds of glass art from local artists and is well worth a visit.
I'm sure others will chime in with their favorite spots but the list above could keep one busy for a week or more.