This is what Alaska Airlines has to say (just in time for the Olympics! When one goes to the US (at least for Seattle flights) from Vancouver one goes through US customs before getting on the plane - I have been through this a few times but have not noticed if this operation has anything to do with Transport Canada, mentioned below):
Travel Advisory
New International Security Directive
The Transportation Security Administration (TSA) has issued a new security directive affecting flights departing international locations arriving in the United States. For Alaska Airlines and Horizon Air passengers this affects flights coming from Canada or Mexico into the United States.
Passengers traveling from Canada or Mexico should arrive at the airport a minimum of 2 hours before departure in order to help with the additional security measures.
* Additional Searches: All passengers flying into the United States will be searched at the departure gate, in addition to normal screening at security checkpoints.
* Carry-on Luggage: From Canada or Mexico, carry-on luggage will also be searched at the departure gate. Transport Canada has limited the number of carry-on luggage to one (1) through the security checkpoint for passengers traveling from Canada to the United States. To minimize boarding delays, passengers are encouraged to check all their luggage. Alaska Airlines and Horizon Air will waive baggage fees for items checked as baggage that the passenger otherwise would have taken aboard as carry-on baggage from Canada or Mexico.
* Additional Inflight Security: Added security measures while on the international flights are also being put into effect.