Well I have been in Iraq since before 2008 so I have yet to file my taxes. By the way I'm in the Army. Anyway, I was married in April of 2007 and since then I have listed as having one dependent. The problem is my wife does not have a SSN yet. We are still in the process of getting her a green card. So when I return from Iraq in 2009 I will have to file taxes for 2007 and 2008. If she still does not have a SNN or green card when I return can I still file her as a dependent or file as not having a dependent and being married? And if I can't do either if these can I be penalized?

If you are married, you can file joint return even when your wife does not have SSN. You will complete and attach W7 (Application for Individual Taxpayer Identification Number) with your tax return.
Also wife is never a dependent, you can file joint return so that you get double standard deduction and double exemptions.