The most legendary one of them all (or at least, one of the most legendary):

"This room is an illusion and is a trap devisut by Satan. Go ahead dauntlessly! Make rapid progres!"
Thought you completed Ghosts n' Goblins? Nah, you got to do it again, sucker!

DRM and copy protection are intentional I guess. Biggest trolling ever. ;-)

I got the idea because of the "degrading game" copy protection schemes which are actually really trolling the (assumed) pirates. Your guns don't work, healing potions poison you, the screen light up in all kinds of colours like you're on drugs. It's an hilarious idea, until it affects the wrong people who really bought the game - happened to me three times.

The NPC in Pokemon Pearl/Diamond/Platinum that trades a Haunter holding an Everstone.

Troll games like Syobon Action, of course. (I could count troll levels in games like Mario Maker.)

Might and Magic 2 has a really evil one that I'm going to spoil here because I think it's better to be spoiled about it than to suffer its effects. If you steal Murray's treasure, at first nothing will appear to happen, but something did; the base values of all your stats are now 3. The current value is not affected, so nothing will be amiss at first, but after you fight a battle or rest, the effect will become apparent at that point. Thing is, a player will likely just check their stats immediately, notice nothing out of the ordinary, return to town, then go to the inn, at which point the game is saved with those horrible stats. While it *is* possible to get your stats back up (stat boost events in MM2, unlike later in the series, don't have any limits other than not working when the stat is too high), doing so could take a while and the game is significantly less fun with those terrible stats.

There's some trolling later in the series (like a certain alter of ultimate evil), but nothing that bad; the effects are usually immediate and often result in at least one character dead or worse. There is a nasty one in MM3, however, with something that makes time pass a year at a time, making your characters age in a way that can't be reversed.

Also, The Hitchhiker's Guide to the Galaxy is also known for being rather trolly; there's a famous Babel Fish pussle that I've heard about where you think you've solved it, but turns out there's something more you need to do. (Plus, it requires an item that, if you don't have at this point, you can't go back and get.) (Also, try sleeping in at the start. This will kill you, but the message it gives is the sort that will strain your suspension of disbelief, but it certainly feels like the sort of thing you'd read in the book on which the game is based.)

Like Unfair Mario?

I've seen videos of that game, and I think it's a poor example of that type of game. Syobon Action is a much better game, and is the troll platformer I tend to recommend.

There's good trolls, and there's bad trolls; Unfair Mario's trolls are bad, as they're just not that interesting or funny enough, especially since there isn't enough variety in them.

Batman Arkham Asylum the "Dead GPU Trolling", almost shit my pants when I saw that one!

Can't think of anything specific off the top of my head, but I love when RPGs have skill check alternative options that are actually worse choices than the default.

Eternal Darkness: Sanity's Requiem (Gamecube) has some great trolling moments if you let your sanity meter get low.
Starts with simple changes like tilting the fixed camera to off angles and adding weird alien chanting to the soundtrack. But will get much more interesting when your sanity is almost non-existent. Don't want to spoil any of the particularly fun effects in case someone plays it down the road, so I'll just say....

"This can't be happening!"

Not Whimsyshire ?

The Secret of Monkey Island had the infamous stump joke

The chainsaw without fuel in Maniac Mansion.

One of my favorite trolls happens in Might and Magic: World of Xeen (spoilers for the Dungeon of Death, but not for the final floor, which would be an even bigger spoiler to describe, as it's bizarre). It goes something like this, though I don't remember the exact order of the first two alters or the exact name of the third:

You find an "Alter of Minor Evil", destroy it, get some XP.

Then, you find an "Alter of Lesser Evil", destroy it, get some more XP.

Then, you get to an "Alter of Greater Evil", destroy it, and get even more XP.

Finally, you discover an Alter of Ultimate Evil, destroy it, and...

You get a message about the dungeon collapsing, with you in it, followed by the Game Over screen.

(Note that if you have Clairvoyance active, which tells you whether it's a good idea to say "Yes" to a Yes/No decision, it will at least indicate that destroying that last alter is a bad idea.)
That makes me think of the one in SaGa 1, which will not work on anything it's supposed to. (It *will*, however, work an anything it's *not* supposed to, however.)

Also, in SaGa 1, if you confuse an enemy that has a melee physical attack, its melee attacks will hit your entire party.

(Worth noting that, though these are obvious bugs, the WonderSwan Color version behaves the same way. Also, Romancing SaGa: Minstrel Song makes a reference to SaGa 1's chainsaw.)

Final Fantasy 5 has a late-game chest with a superboss inside, who will likely do 7000+ damage to your whole party.

Also, Etrian Odyssey 2 has some squirrels found in the dungeon, which will steal a Warp Wire (Ariadne Thread in later translations but they were still constrained by number of characters for EO2) if you pet it. If that's the only one you brought, you can no longer warp out of the dungeon.

The fact that thugs in Pathologic are able to throw their knives at you. I have a feeling that every player who plays the game has been trolled this way during their first encounter with a thug at night.