I am on h1b and my wife on h4.. I do not satify 183 days of substantial stay.. miss that by 3 days.. will I not be allowed to get exemption for my wife...

If you were in the U.S. for the month of December, you can file jointly with your wife and you boht choose to be treated as resident aliens for ALL of 2006. Check out IRS Pub 519 for process; page 8 I believe.