I was on H1B visa. Wife was with me from Feb 2006 to Dec 2008. Then she left for India and never returned. I also returned to India in Jan 2010. So for the tax year 2009 can I file return as "Married Filing Jointly" or it has to be "Married filing Seperately"? Please note wife was working in India in 2009

You can file joint return as residents. You will get standard deduction of $11,400 and exemptions ($3,650 each) for both of you.
You must both declare your worldwide income for 2009. If you have any foreign income, and on that income you paid taxes in the foreign country, then you can claim foreign tax credit (Form 1116). Your U.S. Tax Return: U.S. Citizen or Resident with Foreign Income

You will complete forms W7 (application for ITIN) for your spouse and children and attach with your tax return.