Guybrush's beard in the original version of this game is probably about as much of a Badass Beard as he could ever realistically hope for. The Special Edition reduces it to wispy fuzz that barely even qualifies as a beard at all, but this leads to some Hilarious in Hindsight moments since Guybrush spends the whole game talking about how much effort it took him to grow his beard, when it's barely even noticeable (which Wally eventually calls him out on in the sequel).
Speaking of which, Guybrush's beard and longer hair in the original version give him an odd resemblance to Qui-Gon Jinn.
Towards the end of the game, LeChuck claims he has a surprise for Guybrush. One if the dialog choices for a response is "I don't suppose it's a Nintendo game..." (Changed to "LucasArts game" in the Special Edition) About a decade and a half later, Guybrush would appear on a Nintendo console.
Nightmare Fuel: Until Tales was released, this was unquestionably the scariest of the series. For specific examples, see below.
LeChuck chasing Guybrush around with a voodoo doll in the tunnels beneath Dinky Island is terrifying. While you're desperately trying to solve the last puzzle of the game, there's this dread that at any point, LeChuck could come in and send Guybrush screaming in pain into the next room. For a little kid trying to finish the game while being forced to watch the loveable pirate being tortured, this game is an anxiety-inducing masterpiece.
Guybrush's parents come back in his dream, and then their skin melts off. Then the scene goes funny again when they start dancing. But the scene goes scary again when LeChuck shows up, turns into you, and then kills you the same way you killed him in the first game. It's not exactly The Exorcist, but it can be pretty freaky when you're a kid.
Dominic Armato really sells being boiled in acid in the Special Edition if you fail to solve LeChuck's Rube Goldberg Device quickly.
Squick: Seeing Governor Phatt, his grotesquely obese body lying in bed, with some ugly goo being constantly fed to him through tubes.
They Changed It, Now It Sucks: A surprisingly large amount of fans were upset that the Special Edition omitted the original version's title sequence, even though it would have been slightly redundant when you can listen to the main theme in its entirety in the main menu. The Bone Song's music was also out of sync with the lyrics. A patch released on July 29 restored both the original intro and credit sequence for the classic version, as well as addressing the issues with iMuse music and sound effects and fixing the lyrical sync with the Bone Song; interestingly, the intro is fully voiced, meaning that they had at least planned on making an HD remasterization of it, one can only hope they do it in a future patch...
Much like in the game's predecessor, the Sam & Max cameos were removed because of copyright reasons, although in the case of the previous game, the Sam & Max totem was at least replaced with one in the likeness of Purple Tentacle...
Unwinnable by Insanity: Early versions allowed Guybrush to get the 6000 pieces of eight needed to hire Kate Capsize one at a time by polishing the peg leg of one of the Men of Low Moral Fiber.note It would stop giving money once you reach a certain amount, but you could delay that by buying things from the antique dealer, which could later be sold back at full price. Doing this bypassed learning the trick to winning the spitting contest, which was later needed to escape from a death trap. The special edition fixes this by capping the number of pieces of eight Guybrush could earn this way far, far lower.
Values Dissonance: Apparently it's not acceptable to make jokes about white slavery anymore.