How do you format a popular reference in writing?

By convention, the title of a work is italicized. However, the names of products or characters are not not. So if you're talking about an Etch A Sketch, you don't need to do anything special except capitalize it. Super Mario is italicized if you mean the video game, but it's not italicized if you mean the character.

Edit: the answerer below is a little too conservative. It is perfectly fine to mention real products in your fiction, and you can have your whole story be based around them, as long as it's clear that it's fictional. You may also make reference to other people's creative works, but you can't write your own work based on that. (That is, you can mention the game Super Mario, and you can have your entire story revolve around the main character wanting to buy the game, but you can't actually write your own Super Mario storyline.)

This isn't a question of citation or grammar, but rather of trademark and copyright. Many brands and commercial figures/icons can't necessarily appear in works of art without permission from the company, because in the company's eyes, the artist is just profiting from the marketing draw of the brand, so they deserve a cut from the profit the art pulls in.

In the case of your first two metaphors, those are fine, because they're not basing your story around those characters. In the third example, the Etch a Sketch is the central figure in the story, so it might be iffy, but if it's in passing, it should probably be fine.