Due to a confusion of resident alien status, my company (on my request) did not pay FICA/medicare for the duration of F-1 OPT in 2007 (01/01/2007-09/30/2007), even though it appears that I should have paid it because I had been a f-1 for longer than 5 years and would be considered resident alien. I was under H1-B from Oct-Dec and my FICA/medicare was deducted for that period. How do I pay the unpaid FICA/medicare when filing my 2007 taxes?

I am going to file as joint resident for 2007 using turbotax.

You don't need to worry about the FICA taxes during OPT.
To file joint return as resident for 2007, you must wait till you meet SPT in 2008. You will also attach a statement that you want to be treated as residents as First Year Choice. You will both report your worldwide income for 2007.

MukatA:

This time, you are in error.

Since Vvume has been in country for more than five years, the exemptions under the F-1 visa no longer apply. Hence, he is a RESIDENT alien and IS liable for FICA taxes.

He has the legal obligation to tell his employer this fact and then the employer has to make arrangements to collect and pay the FICA taxes NOT collected during his OPT period.

Yes, you are right.
My question: For F1 visa holders does the 5-year exemption period includes the OPT period?

Yes, that includes the OPT period.

The 5 year exemption period is full and final, I am not sure. The tax treaty has different exemptions.

This is from publication 901 for Students. While there is clearly a fixed 5 tax years limit in case of France, there is no such limit in case of India.
For India: The individual is entitled to these benefits only for a period considered reasonable or customarily required to complete studying or training.
For France: An individual is entitled to this benefit... for a maximum of 5 tax years.
The treatment for students from India is not same as that from France.

Here is about J1 exemption for teaching and research for most of the countries.
"... is exempt from U.S.income tax on income for teaching or research for a maximum of 2 years from the date of arrival in the United States."

The above statement does not have the words "2 tax years." That means the two years on J1 can be part of 3 tax years.

Agreed.