Ravi:
Download IRS Pub 519 from
www.irs.gov and read page 6. If you are in the profession that makes you exempt under a "J" visa, then you cannot file jointly.
If not, then you both clearly qualify under the Substantial Presence Test and you can file as a resident alien using Form 1040. That will allow you to file jointly.
If the SSN does not come in by 17 April 2006, but you are entitled to a refund, just mail in Form 4868 to request an extension, then file when the SSN finally comes in.