It does not matter that your wife doesn't have a job but if she has been outside Canada for 2 years, even on a tourist visa, I don't think you can consider her to be living in Canada. Living outside Canada adds the burden of proof that you will be moving to Canada when you get your PR. Such proof could be having arranged housing, having a job offer, acceptance to college or at least some letters from relatives supporting your plans and offering a place to stay while you look for housing and some of your own plans as to where you will live and what you will do in Canada.
If you are tourists in Thailand, you can not apply through the visa office there. You can give a mailing address in Thailand but you must apply through the visa office in the Philippines.
Yeah, I think that she should be living outside Canada. She actually went back to Canada last Nov 2009 and came back here in Thailand on February 2010 - it's still more than a year though. There's no problem with the place because she has a sister there where she stayed when she went back and who is also very willing to accomodate us. My worry is that the application might be delayed because of the residence issue. They might be looking for any visa to support our stay in Thailand. What we want is to expedite the processing and avoid any reasons for delays.