Many video game developers work their entire careers to have the opportunity to make a game involving popular icons such as Batman, Spider-Man, or Godzilla, but if those opportunities can't be earned, why not just take Batman and make him your own? Hardcore Gaming 101 has put together a fun list of games that, ahem, "borrow" famous characters that, legally speaking, really should not be there. The king of this kind of thing has to be Sega's The Revenge of Shinobi which runs wild with unauthorized cameos and, as a result, has been revised many times over the years.
The Revenge of Shinobi is probably the most famous game for these type of changes, with numerous revisions. REV00 was only released in Japan and has enemies that resemble Rambo, Spider-Man, Batman and Godzilla. REV01 changes the Rambo enemy (by removing his bandana and making him bald), and Batman (by making him resemble the manga character Devilman). However, the Spider-Man enemy originally only looked kind of like the comic book character, but here he was redrawn to look exactly like him. The REV02 version included a copyright notice for Marvel, indicating that his appearance was official. This was done because Sega had the license for Spider-Man arcade and console games, so they decided to go for a bit of cross promotion. REV03, which appeared on compilations, changed the Godzilla boss by turning it into a dinosaur skeleton. The final revision, released on the Wii Virtual Console, changed the Spider-Man enemy’s color to pink, and changed the ninja on the title screen to less resemble Sonny Chiba.
There's a major difference between an indie hobbyist thinking he's going to make the next Metroid game without Nintendo noticing and a professional outfit like Sega deciding to just co-opt Batman and Godzilla for the hell of it. In a strange way you have to admire the chutzpah of it all.