The summer car ferry from Seattle to Victoria, the Princess Marguerite, has been dropped. The voyage was four or five hours each way and with just the one round trip daily, they couldn't make a go of it financially.
The Washington State Ferry trip through the San Juans over to Sidney is beautiful but very oversubscribed in the summer! If you can't get to Anacortes hours ahead of time and cool your heels, the best bet is to drive up I-5, cross into Canada at Blaine, and take the BC Ferries trip from Tsawassen. More frequent trips, more reasonably priced.
The Victoria Clipper, the high-speed, no-cars ferry from Seattle to Victoria, is good fun... but if the sea is choppy it's really an E-coupon ride. Sometimes people stumble off there looking positively green.