I am in US since May 2007 on h1B status. At that time I asked my employer to deduct my taxes as a married with 2 dependents (wife and son).
Now due to some problem, they will not be joining me in US.
I asked one of the CPA, he told that I may file married but separately which I too want to do and the other one told that I need to change my status from married to single.

Which way I should go..

I know I need to pay due tax in all the cases.

Regards

You should file 1040 (because you meet substantial presence test) as married filing separately (you cannot file single as long as you are legaly married).