For 2009, he was a resident alien
For 2009, he was a resident alien due to exceeding the five-year exemption period.
For this reason, he CANNOT claim an exemption from FICA (Social Security and Medicare) taxes for 2009.
You can file jointly with your husband and you will CHOOSE to be treated as a resident alien. This will allow you to claim the $11,400 joint standard deduction plus two $3,650 personal exemption (for yourself and your husband).
Your husband does NOT qualify for the $5,000 treaty exemption because he was no longer a student, even though he was on OPT in 2009. He COULD have claimed it past the five-year exemption period, but that claim was forfeited when he applied for H-1B status, because that action invalidates any claim for a "closer connection" to his home country.
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