We do the Final Wasteland, and Gloomweaver.
Raptor Bot I always throw down a Grimlock impression, "Raptor Bot no like Omnoitron!"
As Visionary when I use Precognition I alway say "and that's half the battle," a somewhat convoluted GI Joe reference.
Close Quarters Combat will often get a "now it's time to fight with Knives!" often followed by the Knifing around song. (Space Ghost reference)
Tempest gets tons of Lost Skeleton "On Marva we call lightning. . . " jokes.
The above has led to emphatic cries of "You can't make aliens dance" when Adept tries to buff Tempest.
The Tumbleweed from Time Cataclysm gets the "OH NO, THE TUMBLEWEED!" panic and freaking out. We frequently then prioritize destroying it with environment destruction effects, I still don't think we've ever attacked it, but it did get End of Days played on it, and once chastised.
"You suck Legacy" is a common theme in our games, with Iron Legacy or the Hero version, usually after he draws a card we don't need him to have, or IL pounds us, It has been directed at Champion Bot a few times as well.
I have a firend who can't help but sing "who'll stop the rain" whenever Tempest heals.
We definitely do refer to the card from Dawn's deck as "That Card," it shall not be named.
"For America!" gets called a lot with Legacy playing.
Stealth Bot is "Bot, Stealth Bot." when played.
Oh, and for some reason Throat Jab tends to get a "Crotch Shot" when it's played.
Lots of singing and wierd refrences in our group, the above are the decent and reasonably humorous results, it gets much worse.