In the BIT.TRIP series, the players themselves are forced to kill CommanderVideo to beat the Recurring Boss Mingrawn Timbletot. Given that the series is a metaphor for human life, it's believed this actually is symbolic of the protagonist being Driven to Suicide.
Each level in the six games is named for part of the player character's, and general human, development, and something it learns. In the fifth game, in which CommanderVideo dies, he is made to learn "patience, frustration, and anger" just before his death.
The sixth game begins with simple geometric shapes, representing each of the friends and love interest made during the course of life, drifting away as the player character futilely tries to keep them together as he dies.
Patapon looks like a cute rhythm game where you command a bunch of eyeballs by inputting commands to have them advance, attack, defend, retreat, etc. You march along, wrecking anything in your path, before you come across the enemy leader Gong the Hawkeye. Who immediately proceeds to lecture you about all the things you've broken and all the Zigotons you've killed. Yeah. You killed a lot of them.
It isn't an effective player punch on its own, but there's a recurring enemy Zigoton called Makoton. In one of the early levels, you kill his partner Aiton, and he vows revenge. He pushes himself more and more until he sells his soul to demons just for a chance to get revenge against the army that took his partner away from him, and he doesn't even get that. You slay him, and he laments that he will never be able to see Aiton again. It's a sobering moment for a fairly upbeat series.
In Patapon 3, it's heavily implied that Madfang Ragewolf is Makoton, brought back yet again with a mask and with amnesia. He apparently starts recovering his memories. And then Sonarchy and Covet-Hiss order him to be executed. Makoton can't catch a break. He's never canonically seen again, unlike The Patapon Princess and Gong the Hawkeye.