Nitin:
Since you cited the Indian Tax Treaty, I assume you are an Indian national.
Since you are are still on F-1 visa status, you should file Form 1040NR. The time spent in the U.S. while under a F-1 visa does not count towards the Substantial Presence Test. You can refer to IRS Pub 519 (which can be downloaded from
www.irs.gov) for details.
Since you are an Indian citizen, you can both claim your wife as a dependent and claim the standard deduction, which I believe is $5,000 for 2005.
However, to claim your wife as a dependent, she will need a Individual Tax Identification Number (ITIN). This is done with the W-9 form, which can also be download from
www.irs.gov. Read the instructions that comes with the form carefully. If it is too confusing, get professiolnal help, both with the W-9 and filing the tax return.