...I'm actually not much of a gamer and ALL of these schools come from comic books, webcomics, movies, televisions and or novels. They may have appeared in games, but absolutely didn't originate there. In fact, if you can FIND a good Ender's Game Battle School FPS or old-school platformer, please let me know.

The Banzai Institute was a standalone research facility, not a school. They maybe had some lower-tier guys doing post-doc placement there, but this was far from a student facility. Says so right on their website: http://www.banzai-institute.com/0401abot.html

I'm VERY familiar with LastExitToNowhere (I've been pining for a Porkchop Express shirt for ages) but other than Hill Valley High School, none of their designs refer to actual schools, and to my mind HVHS doesn't crack the top ten most interesting fictional genre educational institutions.