I am an Indian and I worked in US for a couple of months last year. I am married but my wife did not travel to US. While filling the tax return should I file as single or married filing separately. If I select married filing separately an online tax filing website is asking for my spouse's ssn which I don't have. Please help me with this.

You CAN file as SINGLE if you were separated from your wife for more than six months.

However, It is probably most advantageous for you to file jointly with your wife, filing Form 1040 with Form 1116 to claim the Foreign Tax Credit.  Form 1116 is required because you must claim ALL world-wide income earned in 2012, including any income your wife may have earned, and the Form 1116 allows you to claim a credit for the income taxes paid to your home country.

You will need to apply for Individual Tax Identification Number (ITIN) for your wife by submitting Form W-7, and that process has undergone some radical procedural changes this past year.  Instead of the simple notarization process, the IRS now requires that your home country certify the photocopy of your passport as a true copy.  This is due to rampant fraud in the ITIN submission process.  The notaries simply cannot tell the difference between a fake passport and the genuine passport.

This certification can be done by the Indian (I assume you are from India) embassy in Washington, D.C. or at one of the consulates in San Francisco, Chicago, Houston or New York.  Assuming you do NOT want to drive there, you need to call the nearest consulate and arrange to have this process done via the mail.  Since you must wait until June to file, you have time to get this done (the process, done via mail, can take up to three months to complete). My clients to date have had the best results by mail with the San Francisco consulate, getting the certified passport photocopies in less than 3 weeks.

Also, the IRS recently announced the opening of Tax Assistance Centers through which you may be able to submit the tax return, Form W-7 and passport photocopies IN PERSON without having to get the photocopies certified by your home country consulate. The list of the TACs are at the link below:

Taxpayer Assistance Center Locations Where In-Person Document Verification is Provided

The alternative is to mail in the actual passports themselves, something most of my clients are reluctant to do.

Most probably you need to file nonresident tax return.
What visa did you have? When did you enter and leave U.S. We need this info to provide exact answer.

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Originally Posted by MukatA

Most probably you need to file nonresident tax return.
What visa did you have? When did you enter and leave U.S.? We need this info to provide exact answer.

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I have h1b. I came to US in Nov and left on Dec last week

You can only file nonresident tax return. You cannot claim exemption for your spouse. You can claim itemized deductions for travel, meals and lodging expenses during your stay in U.S. Use Form 2106 or 2106-EZ to figure your allowable expenses that you claim on line 9 of Schedule A (Form 1040NR).

MukatA has it right; you will have to file as a non-resident alien, filing Form 1040NR and Form 2106 to claim your daily living expenses.