For Nintendo:
I know I'm missing a lot (there are a few specific ones on my mind I can't remember) but here,
X, Shin Oni Ga Shima, Doshin the Giant, Cubivore, GiFTPiA, Jam With the Band (Daigasso Band Brothers), Electroplankton, Famicom Detective Club, Chōsōjū Mecha MG, Captain Rainbow, Devil World, Panel de Pon, Kuru Kuru Kururin, Gyromite, Trace Memory, Nazo no Murasame Jō, Stack-Up, Eternal Darkness, Professor Layton, Fluidity, Disaster: Day of Crisis, ASH: Archaic Sealed Heat, Odama, Magical Starsign, Anticipation, World Class Track Meet, StarTropics, Battle Clash, Battalion Wars, FlingSmash, Zangeki no Reginleiv, Hotel Dusk, Doki Doki Panic, Gomoku Narabe Renju, Ice Hockey, Volley Ball, Joy Mech Fight, Soccer, Urban Champion, Endless Ocean, Elite Beat Agents/Ouendan series, Pro Wrestling, Golf, Tennis, Pinball, Hogan's Alley, Baseball, Wild Gunman, Gumshoe, Famicom Grand Prix,Fortune Street, and Magnetica. I did a decent amount of research to confirm most of these as Nintendo-owned.
I believe Pandora's Tower and The Last Story count, but I'm not sure. No idea regarding Xenoblade Chronicles, leaning heavily on no.
Brain Age is listed twice, but not Big Brain Academy.