You are required to file within 3 1/2 months following the end of the tax year! Thus, your 2006 Tax Return would be due April 15, 2007, however you could request a 6 month extension, which would take you till October 2007.
I am not sure where you got this idea that you had 3 years to file your tax return, or that the due date for your 2006 tax return was 3 years, leading you to incorrectly believe that you had till the end of the 2009 to file that tax return.
Unfortunately, the problem is that you did not consult a tax professional and now you would be assessed late filing penalty, late payment penalty and interest on the late payment. I am hoping that you have at least paid the estimated taxes related to your 1099-Misc income generated in 2006.
Now, the Federal and State (CA) will prepare a tax return simply based on your 1099-Misc income without giving you any deductions that you are entitled.
So, I would strongly advise you to contact a CPA or other Tax Professional that you may have been dealing with and have them immediately prepare your 2006 tax return. The tax professional will certainly take all the deductions and exemptions that you are entitled under the law and this will definitely lower your tax liability for 2006!