Wayne Enterprises is a company featured in Batman vs. Teenage Mutant Ninja Turtles. It is owned and run by Bruce Wayne, and maintains at least one large building in Gotham City with advanced laboratories. It was one of several corporations responsible for technology that was needed by Shredder and the Foot Clan, and was the last that they targeted.
However, Batman had anticipated the impending theft of Wayne Enterprises technology, and had sent an experimental cloud-seeder to a corporate ship in the bay. He also created holograms of the personnel and equipment in order to fool the enemy ninja, having evidently sent away the real scientists. After fights with Shredder and the Ninja Turtles, Batman retreated to Wayne Enterprises to analyze the DNA left on Raphael's sai.
At some point, the Wayne Enterprises ship was robbed by the Penguin, who obtained the cloud-seeder.