This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Hey You, Pikachu!
The Haunter in Little Lost Poliwag.
And when you and Pikachu are camping at night and a Haunter shows up. Pikachu shakes in fear until told to use thunderbolt.
Any time you catch a HUGE fish in the fishing game. It practically fills half the screen. Even Pikachu freaks out sometimes. It's even worse if it's something harmless, like a Magikarp.
Even worse if it's as the sun's setting.
Pikachu can slip and fall in the water when looking for Poliwag and get swept away. Pikachu cries out in panic and then disappears. Professor Oak says Pikachu washed up on the shore but for a while it's like Pikachu drowned.