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Mine is hands down the green alien fart cloud in The Pandora Directive. For three simple reasons:
- I don't like being chased.
- I don't like being on a timer.
- It scares the crap out of me to this day.
I usually panic to the point where I forget everything I need to do, despite having played the game a million times, and I spam the everloving hell out of the hint system.
Runner-up, also from the Tex Murphy series: the GRS "eyeball droid" in Under a Killing Moon. For some reason Access just felt compelled to put one pants-crapping sequence into each of these games...
Mazes, particularly the kind with some randomized effect where cardinal directions don't matter anymore. The bamboo thicket in LSL 3 was particularly egregious because you die if you run out of water (limited turn count). They suck in every game, yet every game that comes after somehow looks at what has come before and says, "Oh, we better put a maze in the game, that's what everybody else did." And it's always idiotic. But the one that most stands out to me is Gabriel Knight 2, because the game is such a tour de force up to the end, and is FMV done right, then you get a pointless maze chase scene for the finisher.
Oh god, that thing at the end of GK2... I always use a walkthrough for that, because that sequence cam go to hell.