The Machinima "Beans". Firstly, it crosses over characters from three different series and is made by three different machinima directors, then the storyline involves various internet memes... Oh. And it's made on Super Smash Bros.. Making it a crossover on a crossover.
The Spelljammer and Planescape settings were designed with this in mind. Spelljammer in particular has rule books dedicated to detailing the Crystal Spheres of settings such as Krynn, Abeir-Toril, and Oerth. Where as Planescape has portals to every type of world imaginable.
Similarly, the Hero Clix tactical miniature combat game works on a Point Buy System basis and includes characters from many comic books (Marvel and DC, but also "indie" ones); Superman, Dhalsim and Dark Phoenix against Dr. Manhattan, Beta Ray Bill and someone else to match character points is a perfectly reasonable battle.
Ani-Mayhem, a Collectible Card Game produced in the middle 1990s by Pioneer Entertainment that set characters from many different anime settings — surprisingly including many series licensed by companies other than Pioneer — in a grand romp across their various worlds.
TV Tropes' own Trope Pantheons. Characters from across all fiction gather together as deities, and presumably alternate between annoying each other, and fighting the villains.
So Who Wins, a any character battle website which a crossover between anything can happen.