Didnt knew any besides that one before found this article.
For those who do not want to click:
- Nemesis mechanic by WB (expire 2036)
- Mini-games during loading screen by Namco (expired in 2015)
- Ping system - like pinging on the map so your team mates can see or pay attention to it. EA (expires 2039) FUCK EA
- Dialogue wheel like in Mass Effect - fuck EA (s 2029)
- Direction arrow - racing games, Crazy Taxi style - Sega (expired in 2018 but doubt it will be ever used again)
- Pokemon's fight and catch for later fighting mechanic - fuck Nintendo and Game Freak
- Active Time Battle - not sure, I dont play JRPGs but this one was introduced in FFIV - Square Enix (expired 2012)
- Guitar as a controller for Rocksmith - Ubisoft (2029)
- Mouse controlled flight for aircraft games - Gaijin (expires 2033)
- Plastic musical instruments - Harmonix that was fighting with Konami for the rights (expires 2032)
Nemesis system is probably the most notable because it was a great mechanic that everyone liked. And it is only been used in 2 games and never again.
Edit: Ubisoft and Rocksmith instead of Guitar Hero.