Bomberman (94?) underwater level. Neutopia 2 underwater area.Aldynes when the ship enters and exits the stage.
It's not much, but this boss scales up and down in size: https://youtu.be/v3ZIsMQ222g?t=1389
There's a nice effect on the system card screen when you push the run button in Terraforming (PcE version, at least).
And here's an earlier stage in Terraforming with a subtler, better looking wavy background effect: