off the top of my head i recall there being some fairly obvious nods to Looney Tunes, a couple gags that clearly owed something to Ren & Stimpy, a blatant reference to The Big Lebowski and a dig at the MLP G3 cartoons
Also a noir episode (with Rarity playing two parts at once), an episode that was a parody of Topgun, a fucking DBZ fight in the season 4 finale. The songs in general are pretty 90's Disney, too.
Like, this isn't even getting into how crazy the comics go with references. It went like two pages before Pony Donald Sutherland doing a Body Snatchers gag.
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(idk if that's true but)