Is this the first long form TV show that you've watched? They all use setups from other fiction (movies, other TV shows, or literature) as the basis for particular episodes. Stargate is just more overt about it than most, in part because the modern day premise allows the characters to comment on how the situation they're in reminds them of X (as you noticed).
Also, if you watch genre shows, in particular, there are certain staples that will get repeated among most of them if they go on long enough. For example, having a Groundhog Day style (note that the movie did not originate the concept, it just popularized it) episode is practically obligatory in a science fiction or fantasy show. So the lines are often blurred as to whether they're borrowing from each other after one of them borrowed from a movie, whether they're borrowing from a movie, or both.
Here, you can see for yourself how common the Groundhog Day one is: http://tvtropes.org/pmwiki/pmwiki.php/Main/GroundhogDayLoop
Scroll down to the examples and click on the "Live Action TV" folder.
I can guarantee you'll also find pages like that which list all the places that an idea has been used for any similarity between Atlantis and a movie that you noticed. Nothing is original. Everything is reused, whether intentionally or not. Even the movies that you think of as the source of the trope are usually just the ones that popularized it. You can almost always find examples of it in earlier literature, TV shows, or movies. For example, here's the main trope that "Nightmare on Elm Street" utilized: http://tvtropes.org/pmwiki/pmwiki.php/Main/YourWorstNightmare
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