Sonic the Hedgehog CD It's not surprising that a character like Sonic probably doesn't enjoy just standing around. The iconic Sega CD title took it a little personally, though. Wait long enough without touching the controller and Sonic will start tapping his foot impatiently. Keep it going and he'll just up and decide to leave. He jumps off the screen saying, "I'm out of here" and resets the game. Later in Knuckles Chaotix, waiting idle would actually cause Metal Sonic to show up and attack.
Metal Gear Solid 4: Guns of the Patriots This isn't technically an idle animation, but it's definitely along the same category. During the final fight with Liquid Ocelot, he will at some point grab you from behind in an arm lock. You're supposed to break free, of course, but if you don't, then Liquid will tenderly kiss you on the cheek. This is damaging not because it's likely to send conservative little GamerGater into an emotional temper tantrum laced with slurs, but because it actually restores a portion of Liquid's health. Granted, at that point in the fight, you'd pretty much have to try to be losing, but it does give Liquid a slight edge.
Future Knight A forgotten platformer from 1986 that got ported to the British ZX Spectrum system, Future Knight may actually be the first game to institute a punishment idle animation. Because it amuses me to do so, I will quote Spectrum User magazine from December of that year...
If you leave Randolph standing still for too long a period, he'll wave at you as incentive to get a move on. Leave him in the same spot for much longer and things start to get really desperate: Randolph will go completely bezerk [sic], spinning round and round, flailing his arms and panicking in an astoundingly convincing manner. Ignore him then and the chances are his constitution will plummet at a tremendous rate.
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