I am in H1B, I have two kids,who are us citizens.

1. In 2008 My wife joined me from 19 Sep 2008. Can I fill the tax returns as married filling jointly(she also has SSN)?

2. Entire year(2008) my kids (US Citizens) stayed on India. Are they eligible for child tax credit?

1. Yes you can file married filing jointly.
2. If you are eligible to claim your kids, you will get child tax credit.

My kids didn't stay with me at all in entire 2008. But both are US citizens stayed back in india? Are they eligible for child tax credit?

Did they stay with their mother? If yes, on the joint return you are eligible to claim the kids.

Yes They stay with mom all the time. Thanks a lot for your advice