I came to US from India on F1 visa in August, 2008. In 2013, I was working on my OPT during the first 9 months. Then my status switched to H1B. I am married and I am not sure which tax form should I file? 1040 NR or 1040? Also am I eligible to file taxes married jointly? My wife as an ITIN. Also will I get the standard deduction which the Indian students get even if I am on H1B now? Also Indian students can claim their spouse as an exemption? Will that apply as well? I am confused. Kindly guide me for the same.

On F1/OPT you are a non-resident alien for 5 calendar years, so that would be from 2008-2012. For 2013 you need to use the Substantial Presence Test to determine if you are a residnet or non-resident alien. And assuming yo were in the US the entire year, you would be a resident alien for the entire year and would file a 1040-type form. You can file jointly with your spouse, this would give you one personal exemption each, so 2 together.
As resident alien you are eligible to use the standard deduction. (The tax treaty for Indian students allows using the standard deduction during your non-resident alien period, which other non-resident aliens are not allowed to do).

But for substantial presence test can I count the days on F1 opt from 2012 and 2011? Thanks.

File Form 1040 JOINTLY with your wife. No wait required because 2012 was your fifth year on the F-1 visa, so you met the Substantial Presence Test in 2013.