Asking for the best is such an unfair question. Music is so subjective.
I love how posters were saying The Tragically Hip without putting a song until someone said "At The Hundredth Meridian" at which point they got jumped on as "that's not even the best Hip song" as the previous posters knew that would be the response.
Some of my favourite Canadian songs that have yet to be listed:
"Courage (For Hugh MacLennan)" ~ The Tragically Hip
"Rebellion (Lies, Lies)" ~ The Arcade Fire
"Your Ex-Lover is Dead" ~ Stars
"The Island" ~ The Barra MacNeils
"Good in Everyone" ~ Sloan
"Highway of Heros" ~ The Trews
"Brian Wilson" ~ The Barenaked Ladies
Basically the entire Ashtray Rock album by Joel Plaskett
Does "Wagon Wheel" by Matt Andersen count? Yes it's over played, and yes it's written by Bob Dylan, but Matt's is the best version, the website
www.StopPlayingWagonWheel.com agrees. I can understand why it wouldn't.
That's off the top of my head, excluding songs already listed.