Royal Air Maroc flies Casablanca-New York-Montreal
Pakistan Airlines flies Toronto-New York-Karachi
El Al flies Toronto-New-York-Tel Aviv
VASP Brazillian Airlines used to fly Sao Paulo-New York-Torono. Great JFK-YYZ flights, $125 round trip, too bad they're not around any more.
The El Al flight from JFK to YYZ is scheduled and marketable. THE PIA and RAM flights I am not too sure about. On the schedule boards at JFK, it does state that the flights originate in Toronto and Montreal respectively, however I'm not sure they are allowed to market the flights.
I work at Terminal 1 at JFK, which is where RAM operates, and their passengers on the inbound flights from Montreal are not allowed to stay on the aircraft (I believe before September 11th, the inbound passengers from Montreal, going to Casablanca, were allowed to remain on board the aircraft when it stopped at JFK). However, they must now deplane, clear U.S. immigration and customs, re-check their bags, and board the aircraft again.