So, I don't really know what religion my family is, some sort of Christian sect I suppose, but I always feel nervous when holidays roll around, as I'm an atheist and I know my family always prays at family dinners. They're not super religious, but that just makes me more nervous. This Thanksgiving I bowed my head and ignored everyone crossing themselves when they said a prayer. My question is: Should I fake it or twiddle my thumbs and stare at the ceiling and ignore them this Christmas?
It sounds like your family isn't extremely religious. I would tell them, or talk to a couple of family members alone who you think might be more open minded. Let them know that you don't believe. And when they all pray, you can respect the fact that they are praying, but I don't think you should have to participate in the prayers or cross yourself.
Personally, my family is very evangelical and take their faith very seriously. When they pray for meals or other things, I respect that and stay silent while they do it. But they know how I feel on the issue, and we all love each other and respect one another's beliefs.
What I really advise against, is anything like making an issue out of it and trying to get them all to stop praying or whatever. Just because one person holds certain beliefs doesn't mean that an entire society (yes, even a unit as small as a family can be a society) change their customs because of it. Mutual respect is ideal in any relationship, especially a family. Hopefully yours will understand and respect and love you enough to allow you the freedom to not pray if you don't want to.