Quick Shuttle - http://www.quickcoach.com/ - runs from Seattle to both YVR and downtown Vancouver frequently. Amtrak stops at Edmonds, Everett, Stanwood, Mt. Vernon and Bellingham, so depending on where you are, that can also be a good alternative. http://www.amtrakcascades.com/

Might be off-topic slightly, but if you're one to look at various multi-continent trips, like Circle Pacific or RTW tickets, the current state of the Loonie makes for some pretty good deals, e.g. a business class three-continent Oneworld RTW ex-SEA is US$10,199 and ex-YVR US$7,465; a 22K mile business class Circle Pacific is US$9300 ex-USA and US$5929 ex-Canada.