Set yourself a reasonable margin to make a profit. Take your printing cost per book, and add enough on top of that that you won't have to sell every copy to make back the printing costs.
I've been using local Swedish printers for printing my comics - and for some reason, they've never charged me shipping costs, and I'm not about to complain about that! - so my costs have been kept down, as using an American printer would have landed me with printing costs, shipping costs and toll to pay. I've printed both colour and black and white interiors (always colour covers, though), so the price as varied, but I'll use my completed graphic novel Fathoms of the Sky as an example.
It's 200 pages long, black and white interior on paper that wasn't the cheapest option, but also not the most expensive; full colour cover, perfect bound, with the title printed on the spine. It cost me roughly 5.40$ per copy to print. I sold them for 11$ each, to cover my printing costs, as WELL as the cost of booking a table at the con, transporting myself to the con, and keeping myself fed while I was there. This means I only had to sell half of my print-run to make back the printing costs, and less than two thirds to cover all of my expenses. After that, everything else was pure profit.
Things to keep in mind:
- if you're selling at a small-press con, people will be slightly more willing to cough up the money for your self-published stuff; if you're at a big-name con, they'll be comparing your prices to those of professional publishers.
- People are willing to pay more for colour than for the equivalent length in black and white, in my experience.
- No matter what sort of thing you're selling, you're going to have to talk a good game at the con to get people to buy it. Say good things about your comic and do NOT, under any circumstances, say "I know it's not very good, but...". If they see you aren't confident in the quality of your book, why should they want to buy it?
- Package-deals are attractive! Throw in a bookmark or something in the bundle, and people will feel like they're getting more for their money.