Tax Implications of moving back to Canada?

You're in a sticky position if you have an S-corp, as all the shareholders must be US resident. The fact you have an S-corp doesn't stop you from becoming a resident of Canada for tax purposes using the substantial presence test, so basically you need to dissolve the S-corp otherwise you will be subject to dual taxation.

If you live in Canada, your wife is a residential tie and as you are both Canadian citizens basically you are resident for tax purposes. Can't see how a court could possibly rule that you aren't. Basically you and your spouse are always considered residents of the same country, you cannot be residents of different countries for tax purposes (otherwise everyone would make their wife resident in Monaco for tax purposes and put everything in their wife's name).

The CGT exemption in the US is irrelevant as you are resident in Canada for tax purposes, so you pay Canadian CGT on the sale of the home and there is no exemption like there is in the US. You certainly couldn't maintain US resident tax status for any length of time. From the sounds of it your home in the US ceased to be your principal residence on the date you moved to Canada, so you would pay CGT on the capital gain from that date. (Which will probably be zero given the current market).

What you originally paid for it isn't relevant as the time you used it as your principal residence is exempt from the calculation as CGT is not applied in that case (unless you're over the US limit, I forget what it is, $250,000 or something like that?)

Given that it's nearly the end of the year, you can save yourself a lot of paperwork by moving your tax home on January 1st, then you don't have to file dual-status and you can file a 1040 for a complete year and not pro-rate your personal exemptions. Then you tell them you've left using 1040-C and dissolve the S-corporation on December 31st as well. Then for 2009 you simply file a T1 for the whole year.

IRS publication 519 explains dual-status returns, which are best avoided if at all possible. The CRA and the IRS also have various publications explaining how CGT works.