In-game, I don't usually bother with non-damaging moves outside of one or two paralyzing and/or sleep moves to assist in catching legendaries. Most story battles simply aren't long or difficult enough to warrant a lot of setup with non damaging moves when a quick assault would work just as well.
For more intense battles, however, my team is set up with a few non-damaging moves. Thunder Wave, Agility, Roost, and Haze are among them. These have served me well since they give me a variety of options, ranging from disabling my opponents to restoring my HP.