I have taken notice of many Sci-Fi Movies and TV shows that seem to have a common thread. There seems to be alot of religion of all kinds being pumped into Sci-Fi. Examples are Terminatorwith it's apocolypse view, SG franchise with it's false gods, Supernatural need I say more, the new upcomming Sci-fi channel show Sanctuary and many more.

Has anyone else seemed to notice this influx of religion in Sci-Fi?

I have noticed it since I first started reading sf. Robert Silverberg retold the Gilgamesh epic, Robert A Heinlein mined the Bible extensively for his stories and novels (and one of his most popular characters was named Lazurus.)
It's way of allowing us to face our demons, both personal and societal, without admitting that we need a Higher Power. Plus it's a good way to make us think outside the box where religion is concerned.
If you question God, you may be condemning yourself to Hell. But if someone approaches organized religion the way Heinlein did in Stranger In A Strange Land, then you smile and wonder what it would be like to grok completely and be able to say "Thou art God!" But just remember that Micheal Valentine Smith paid the Ultimate Price for his herasey just as Jesus did!

Science fiction authors, on the whole, aren't too terribly good or creative at what they do. Aside from a very select few, authors, most just write derivative crap. It's kind of why you'll almost never see science fiction considered real literature besides, say, 1984, or Brave New World.

So pretty much, they like to take elements from popular contemporaries, in an attempt to cater to their audience. And right now, tying things into religion is popular, because we've got kind of an odd mix of a mostly liberal society that also has strong but uninformed and nebulous religious conviction.