A lot of outfitters sell their used canoes. Selection is usually better in the fall. Here are a couple of links to their pages:

http://elyoutfittingcompany.com/buy-boundary-waters-canoes-gear-supplies.html

http://www.piragis.com/canoes-for-sale/used-canoes-and-kayaks

I know that Spirit of the Wilderness and Voyageur North also sell used canoes in the fall, but either I couldn't find their page or you have to call in the fall.

Spring Creek Outfitters is also a good place to go. They generally have a good selection, but again, it is better in the fall - http://www.springcreek.com/canoes/wenonah-kevlar-canoes

Craigslist can be hit or miss on used canoes. I've usually found, though, that you get better deals through outfitters than on Craigslist.