I am on H1B and working in US since 2.5 years, my wife was on H4, but ttansferred to F1-CPT status in Oct '08 and also has a W2 this year. Is it OK to use a software like Turbotax or other that does not ask for our visa status? We are resident aliens and my wife's W2 has just Federal and State taxes withheld [I guess she gets FICA exemption]. My problem is would turbotax/other general software make us pay more Federal/State taxes since her W2 shows she paid "zero" for SS/Medicare taxes in 2008?

Are you working on joint return as married filing jointly?
Also, complete your return using the software. Do not file unless you are satisfied.

File jointly. If you have filed jointly with your wife in the past, then you can efile, no problem.

If this is the FIRS time you have filed jointly with your wife, she needs to sign a statement that she "chooses" to be treated as a resident alien for all of 2008. That will require that you file by mail.