I was working on my OPT since May to September 30, 2005 .My H1 started on October 1st, 2005. I am from India.

As long as I was on OPT my employer did not deduct the social security and medicare taxes. From October 1st, 2005 , I have been paying these taxes. Should I file my taxes as a dual status alien ( 1040 NR + Form 8843 )
OR

File as a resident alien ( 1040) ?

You can go either way.

If you file dual-status, you can file immediately.

If you file as a resident alien, you must wait until June 2006.