The fly-swatter minigame in Mega Microgame$, as a standard quick minigame and a full version.
In Twisted!, the hardest version of the minigame "Red Delicious?" features the exercising guy who shows up in Mario Paint between the title screen and the main game.
In Touched! 9-Volt has a microgame based off of Mario Paint. Touched! also has a remix of the main Mario Paint music.
D.I.Y. also features a Mario Paint microgame, an Easter Egg involving the Mario Paint music, and the whole graphics editor gives off a Mario Paint vibe.
In the Wii Photo Channel, the Doodle feature makes two references. First, the "Undo all" button summons a rocket to erase all the doodles. The rocket looks and sounds different, but functions exactly like the rocket eraser in Mario Paint. Second, if one holds Down on the Control Pad and hits the eraser, it does undo or redo with the sound of Undodog from Mario Paint.
Mario Maker has already been shown to take many cues from Paint, even the fly-swatting coffee break minigame.