Toy Story 3 doubles as an example of Darker And Edgier within a series, and was an especially memorable case, since it took a series with a reputation for lightheartedness and gave it a Prison Episode.
Even in comparison to the first movie, the sequel is perhaps even darker. Its Villain Song is considered much more intense than that of the first, subjects like child abuse and war are dealt with much more bluntly, and the violence is both heavier and more frequent.
Atlantis: The Lost Empire is also one of Disney's darkest. During the Leviathan Chase scene, a lot of men on the Ulysses die and there is quite a death count.
Wreck-It Ralph, despite most of the film taking place in a candy-themed kart-racing game, has a pretty deep plot, and one of the most vile villains in the Disney Animated Canon.
How to Train Your Dragon wasn't that dark or edgy, but it was more serious compared to Dream Works' other animated films, and it's still Darker And Edgier compared to the book it was based on.
The 2009 made-for-DVD animated film Wonder Woman takes this approach. Wonder Woman is shown killing on numerous occasions, including cold-bloodedly killing several guards (including two who have their throats cut by her tiara). The film also ramps up the sexual innuendo.
Kung Fu Panda 2 is significantly darker than the first film. Multiple characters are Killed Off for Real on screen, (though we don't see their bodies) and the Never Say "Die" rule is broke a LOT, to where it seems like "death", "dead", and "kill" are used every other sentence. The villain wants to take over all of China with giant cannons that are seemingly unstoppable and really are used to kill. And then there's the repressed memories of Po's traumatizing childhood.
Transformers The Movie compared to most of the rest of the series, the original series occasionally took a darker turn but everything usually turned out fine in the end, but in the movie the vast majority of the original Autobots are killed within the first 20 minutes in increasingly gruesome manners Optimus Prime included, later the surviving Autobots (mostly newer characters) band together to save the world from Unicron, a planet eating Transformer, while having to avoid Galvatron, the rebuilt Megatron.
Digimon X-Evolution. When Digimon die, they actually leave their corpses behind, the hero has an attack called "All Delete", and previous heroes are ruthless killers.