What cards go in a side deck?

Answer 1

Typically you put those "just-in-case" cards into your side deck; cards to respond to a variety of deck types. For example, you might include Shadow-Imprisoning Mirror in your side deck for when you go up against a DARK-attribute deck. Including that card in your main deck could prove to be less than optimal if your opponent is not using many DARK monsters.

Another use of the side deck (albeit a rare one) is to radically change your deck. The trick here is that your opponent has already seen your deck once and is using their side deck to counter yours. You can throw him/her off by constructing your deck and side deck in such a way that you know which cards to swap out to make your deck run differently (i.e. taking out your effect damage cards to include out-of-play cards).