So let's start with normal game companies.
Arc Sys and Examu start with a Blaz Blue vs Arcana cross over...flash game. In which you eat Heart, as Arakune.
Dungeon and Fighter makes a dating sim.
TeamLiquid releases a "Professional" mod for Starcraft 2.
Type-Moon characters started twittering.
I'll put more as they come in out of boredom.