Choice 1: File nonresident tax return.
Choice 2: You can file resident tax return as Married Filing Jointly. You will have to wait to file your tax return till you meet the Substantial Presence Test in 2009.
You will get standard deduction of $10,900 and exemptions for both of you and the kid.
You must both declare your worldwide income for 2008. 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) or you can use Foreign Earned Income Exclusion (Form 2555).
You will complete forms W7 (application for ITIN) for your spouse and children and attach with your tax return.
Read about H1-B tax filing:
Your U.S. Tax Return: The U.S. Visas