I can only answer this for the main series games right now. I don't think many side games even have Hidden Abilities in them, but if you really want, I can probably do some research on that. HAs have also only been around since B/W so I'll be skipping all the previous games.
Black/White: Yes. there was an event in Japan only where you could get one if you Pre-ordered the Genesect movie. This was in 2013.
Black 2/White 2: Yes. It's the same event as the one above.
X/Y: Yes. There was an event everywhere last year where you could get one if you participated in Play! Pokemon 2016.
Omega Ruby/Alpha Sapphire: Yes. Same as above.
Edit: Apparently if you transfer Mewtwo to your game from the Virtual Console release of Red/Blue/Yellow, it will have the Hidden Ability. I've never tried this myself though.