I just called the Canadian Embassy here in Bangkok and the person I got was super helpful (especially seein' as I'm an American NOT a Canuck);

Canadian Embassy - Bangkok, Thailand
15th Floor, Abdulrahim Place
990 Rama IV Road
Bangrak, Bangkok 10500
Thailand
Tel: 02-636-0540

She told me, even though you have the Canadian certificate of birth that you need to apply for the baby's Canadian Citizenship card and then a Canadian passport.

She actually is emailing me the information you need, but as of the writing of this it hasn't dropped into my in-box.

Here's the Canadian Embassy's website (the real one, not the b/s ones Google gives you as suggestions!);
Government of Canada | Gouvernement du Canada

The information you need is on there after you click English language and it's under the heading "For Canadians", then the sub heading "Living/Traveling Abroad". On the next screen, look under the heading "General Services During Your Stay" and click "Passport Services". On that page are both the Proof of Canadian Citizenship application AND the Child Passport application form.

The person I spoke to said you MUST first apply for the "Proof of Canadian Citizenship" card (2250baht application fee), and as soon as that application is accepted you can apply for the Child Canadian Passport (2100baht application fee) using your receipt of having applied for the Canadian Citizenship Card, your travel plans, etc as proof you're takin' the child to Canada.

What she said you SHOULDN'T do is use the child's Thai passport to apply for a visa for Canada as a Thai. She said once you follow the correct procedure the child's as Canadian as you are as far as Canada is concerned and as Thai as your wife is as far as Thailand is concerned meaning it'll be both a Thai and a Canadian citizen and hold both Thai and a Canadian passports

Once you get BOTH the Canadian Citizenship card AND the Canadian Passport for the child, you would follow this procedure leaving;
Use the child's Thai passport to stamp out of Thailand, and enter Canada on the child's Canadian passport.

It's done like this ALL the time. There's NO laws broken either by leaving Thailand as a "Thai" or by entering Canada as a "Canadian".

Comin' back here you'd do the reverse;
leave Canada on the child's Canadian Passport and enter Thailand on the child's Thai passport.

Passport Control at the airport isn't gonna bat an eye at this as it is done all the time by half-Thais who hold two passports and face it, you ain't the first Canuck in history to have a half Thai-half Canadian baby.

Good Luck,
P/S: The info from the lady at the Canadian Embassy just hit my in box before this post.

If you want the info send me a personal message and I'll forward it to you or email me at toddaniels at gmail dot com. <-If that email won't display. Just Google; Tod Daniels, Thai language, Bangkok, and you'll find me in there somewhere. My email is at the bottom of all the stuff I write about Thai language schools. .

Sorry this was long, hope it was helpful to you. ..