I got married in Dec2009 but wife will come to US in June 2010, can I file as married for 2009 return

Where you married by Dec 31, 2009
Does she have a tax number to be used to file for taxes

Yes, if you are a U.S. citizen or resident, you can file joint return even when your spouse has never been to the U.S. Attach W-7 (ITIN application) with your tax return.

@Fr_chuck:
Yes, I was married by 31st Dec 2009 and she is not having tax number.

@Mukata:
I am on H1B Visa, I read that for ITIN application I need her notarized passport copy. Now as she is not in U.S. how can I do that?

For W-7, have the copies notarized by a foreign notary. Take the notarized copy to the office that issued the passport. A certification will be issued in the form of an "apostille," which will be attached to the copy of the doucment.