How O-1 visa holder should file his 1040 form and other taxes?

O-1 is work visa. Your days in U.S. are not exempt from residency. Your U.S. Tax Return: Substantial Presence Test
When did you enter U.S.

Agreed; some form of tax return will be needed.

Can I extend tax submission and apply for residency? Since my spouse has no SSN or ITIN for joint filing?

File jointly and apply for an ITIN by submitting Form W-7 WITH the tax return.

You CAN file Form 4868 to request an extension to 15 October 2012, but make sure you will be due a refund. If you OWE money, mail a check to cover the amount owed WITH the Form 4868.