I would like to know what would be the best way for me to file.
Either joint married or married separate.
I have a lot of factors so I will use a professional, but I just want to know what is best.
So here goes.

Me I lived in MD for just under 6 months and VA for the next 6 months.
I worked the same job in both states.
In VA I also worked a part-time job.
I purchased a home in VA and am a first time home buyer.
So I will be itemizing.

My wife live in GA the entire year.
She worked 2 different jobs in that year.

Are there so many things going on to where it would be best to file separate?

Almost always it is best to file as Married Filing Jointly as opposed to separate. One factor that might lead you to file separately is if one of you has significant medical expense compared to his/her income, such that you could meet the 7% threshold for deducting them, but only if you filed separately. Tax software such as TurboTax will automatically determine what the best filing status is for you.

Your state income tax filing will be a bit complicated, as you must file in MD, VA and GA.

Agreed; filing jointly is almost ALWAYS best.

As for filing for the state returns, you need to get professional tax help. While it is complicated for you, an experienced tax pro can handle the complexity with little problem.

If one spouse itemizes deductions, the other must also itemize. So it appears that you should file joint return, which normally results in lesser tax. Also you can do calculations both ways and see which is best for you.

My spouse has lived in Puerto Rico for 2010 taking care of elderly uncles in Puerto Rico after his mom died the end of 2009. I lived and worked in Texas for all of 2010. How should we file this years income tax?

Did he earned ANY taxable income in Puerto Rico?