My Status changed from F1 to H1 in October 2009. I have been in US on F1 since August 2006. Should I file my Taxes as Resident or Non Resident. Do I have to pay the Social Security and Medicare taxes for the whole year, or should I pay them from October?
Please let me know if I have to submit 1040NR or 1040.

If you are not married, file nonresident tax return and Form 8843. You will get treaty deduction if you have income during F-1.
During H-1B, you must pay SS tax amd Medicare tax. H1-B tax filing: Your U.S. Tax Return: The U.S. Visas