Most of the popular US-based part stores will ship to Canada, but some are more "international order-friendly" than others. Here are some sites that I frequent. All of these ship using only USPS now, so you don't have to worry about bullshit brokerage fees like with FedEx and UPS.
http://therealbobroberts.net/ - Charges actual USPS shipping costs. He doesn't accept PayPal or credit cards though, so you have to buy a postal money order in USD, which will cost you about $6 and a trip to the post office. Ordering is done through email only. (although worth the hassle - Bob is awesome)
www.arcadeshop.com - Charges actual shipping costs based on the service you request (e.g. First-Class, Priority) and they take credit cards. Ordering is done over the phone.
www.quarterarcade.com - Minimum $50 international order

, they take credit cards and PayPal, they apparently charge a few bucks over the actual shipping costs for handling/packaging. Ordering can be done online, but they don't give you a final shipping cost until after you place your order.
www.mikesarcade.com - They take credit cards and PayPal and seem to charge actual shipping costs. (i.e. $7 for small items, $25 for larger but presumably via Priority Int'l ) Total price is given during checkout, but you don't get to choose the shipping method.
www.lizardlick.com - Online ordering, payment by PayPal, gives you shipping quotes during checkout and lets you choose which shipping method you want.
www.jammaboards.com - Online ordering, payment by PayPal or credit card, gives you shipping quotes during checkout and lets you choose which shipping method you want.
www.twistedquarter.com - Online ordering, payment by PayPal, gives you shipping quotes during checkout. They only use USPS Priority, so you're looking at minimum $21 even for a $0.25 part.