Let's go step-by-step through this.
1. "brainiac". Ridiculous claim. Brainiac is simply a word, generally used in a slightly sarcastic manner to describe a smart person. It may or may not have come originally from the place you claim, but that's about as strong a link as claiming that someone telling someone else that they were adopted is a reference to Star Wars Episode 5.
2. "no one can hear you scream". Well, I'll admit that Alien may have popularized this phrase, but I'd be willing to suspect it's a lot older than that, and that Alien just piggybacked the concept.
3. "Firestarter". Dude. It's a word. If there was a book called "Car" would you claim that my car is a reference to that book. No. Duh.
4. "cloud". Grasping at straws here. The visual cortex determines processing what your eyes see. So clouding it would have just about as much to do with this so-called reference as me saying that the cloudy day I'm having today "clouds the sun".
5. HGttG. Ridiculous. Please base your speculations in some sort of fact. The concept of people escaping doomed planets is again, much older than that.
6. See #3.
7. Insane laughter is well-imprinted in the public's collective conscious, and has about as much to do with anything particular piece you pick as it does to do with turnips.
8. Fear of rats is old. Older than Lovecraft.
9. Rabbit hole. Now you're getting somewhere.
10. "Sasha! Milla! Lili!" Dialogue of this nature is not particularly uncommon and even IF it originated in the place of which you speak, that's like saying that every single piece of fantasy in existence is a reference to JRR Tolkien, or that every piece of Sci-fi is a reference to Jules Verne.
11. Can't really say about the thing in Milla's mind, don't really recall enough.
12. Ask not for whom the X tolls, it tolls for thee. Again, another good one.
13. Stuff flying through the air. This is probably the most ridiculous one yet. If anything, it's a reference to ACTUAL TORNADOS and not some crappy B-movie ABOUT them.
14. "Chicken of the Sea". Well, Chicken is a rerence to cowardice, and Elton's a sailor. Debatable if the confluence of words has any actual meaning, but I'm siding with coincidence on this one.
15. "Can you hear me". Well, gee. Maybe it should have occurred to you that this sort of language dates back to stuff like the telegraph, and indeed any sort of long-distance communication. It's a sort of "is there anybody listening on the other end" type of deal to avoid lost data.
16. Rising into the light. Old idea. More often associated with angels and God than some old movie about computers.
17. The Godfather. Now we're getting somewhere. Maloof is a pretty obvious parody of the Mafia boss, while his partner Mikhail represents the standard Mafia thug.
18. Don't really know much about the "in this dojo" thing.
19. "The most Dangerous Game". It's an old image, the idea of hunting humans. Not sure if it actually came from the most dangerous game or if that short story drew off of some mythology somewhere. In any case, another good one here.
20. Brains exploding. Again, you're grasping at straws. The idea of raw psychic power causing brains to explode is pretty commonplace, and I doubt it was any intentional reference on Double-fine's part./
21. Revenge is best served cold. Either a misattribution on your part, or another case of "too common to consider a reference". Sources vary.