I lived in the US for the whole of 2008.
I was on f-1 opt from jan - sept 30, and transferred to h-1b on oct 1st 2008.
What tax return do I file. 1040/1040NR?

Thanks

If you are not married, you must file non-resident tax return Form 1040NR or 1040NR-EZ and Form 8843. Your income during F1/OPT is not subject to FICA taxes but you must pay federal and state income taxes. Since you have OPT income, you will get deduction based on tax treaty between the U.S. and your country.
Read: Your U.S. Tax Return: U.S. Tax Filing Requirements for Non-Residents (http://taxipay.blogspot.com/2008/03/us-tax-filing-requirements-for-non.html)