For built-in software, they're used in:
- Streetpass Quest I and II: Two coins apiece for a "wanderer", random color, level 1 or 2, that goes along with miis you've met. It's usually a good idea to max out to have 10 characters in the party whenever you "venture forth". In quest 2 you can also spend 2+level coins to have previously met miis rejoin even without meeting them again.
- Streetpass Puzzle: 2 coins get you a random blue piece of any panel that you've started but not yet finished. Note that this may be a piece you already have.
- AR Games: Unlock game modes and other extras.
- Swapnote / Nintendo Letter Box: Pay 5 coins for stationary.
Additionally, any game can use play coins for in-game unlocks. For example, in Street Fighter IV you can use them to get a random figurine; in Kid Icarus: Uprising you can use them for idol toss eggs.