imported post
I took a 22 cal rifle through Canada to AK, and it wasn't a problem. The customs guy had me give him the car keys and unlock the rifle case after assuring him that it was unloaded and then place the unopened case back in the car. He then told me to wait in the lobby. Presumably he either inspected the rifle on the spot or tooke the case to another location and inspected it. 10 minutes later, he comes back with a form all filled out (type of firearm, serial num, etc, etc) and ready for me to sign saying what type of rifle it was and why I had it (transport to AK). I paid a small fee and went on my way.
In doing the research, I found out that you can get a license to carry as many firearms as you want for one set fee. The Canadians aren't too big a fan of handguns or assault-style rifles like an AR-15... most are called "restricted", but are not "prohibited". "Restricted" seems to mean that they're allowed for certain things (like transport to the USA) but not things like self-defense. Reference
http://www.cfc-cafc.gc.ca/faq/default_e.asp#a3 Notably, any snub-nosed revolvers or tiny semi's like the glock 26 are right out (probably easier to fedex them).
Also you will likely have problems taking high-capacity mags in. My rifle had a 10-rnd mag, which I think was technically not allowed (5-rnd is the max for rifles iirc) but I heard no complaints. Reference
http://www.cfc-cafc.gc.ca/factsheets/visitin_e.asp
While in Canada, I'd keep all firearms unloaded and locked in a case in the trunk.
EDIT: sorry, the links were a bit messed up the first time. fixed now