The Scooby-Doo film was in development since the early 1990's.
The film was intended to be released in 1993 under Universal Pictures, but was then pushed up to 1997, then 2002 under Warner Bros. Pictures. Two different scripts were recently found online in 9/13/2014 on a blog post by a user named loonyscript.
The Craig Titley script is a completely different story than the one we eventually got. It's set in college and up until the first half, it sort of plays out like a pilot episode to the original show (an origin story) in which the gang deals with a usual faux-ghost mystery, but from there on there's an almost sudden, darker change-of-tone that includes real demons, Armageddon and a lost underground ancient city. This half strongly reminiscent of Mystery Incorporated, while as a whole, it's reminiscent of Witch's Ghost (fake ghost mystery followed by the release of ancient evil).
The story in the James Gunn draft is the same as in the movie. Everything's pretty much the same, apart from a few things: there's no Luna Ghost case at the beginning. It starts off with your usual horror film prologue at Spooky Island where Shaggy's cousin Isabel Rogers and her friend are chased by the island demons. Isabel's father pleads his nephew Shaggy to search for his missing daughter at Spooky Island. Shaggy and Scoob manage to pull the gang back together again to solve this mystery, after Mystery Inc. had broken up (told in a montage of TV interviews and such at the beginning, "documenting the rise and fall of Mystery Inc"). There's no Mary Jane character for Shaggy (thankfully) thus no jealous Scooby. The Daemon Ritus is a hardbound text (much like the H.P. Lovecraft's Necronomicon). Mondavarious is still the main suspect and owner of the island but his part is much smaller and less comedic. There's no Scrappy-Doo this time. The whole purpose for sacrificing Scooby is so that the Demon Rex, a "gargantuan, fiery winged beast" can inhabit Scooby's body. The ending is pretty much ridiculous and hard to take seriously (even in the mindset of a live-action Scooby Doo movie). The Demon Rex is defeated, and it's revealed that Mondavarious is actually a man in a mask, who turns out to be Professor Garret Rogers (Shaggy's Uncle), who is revealed to be Fred (!), who is eventually revealed to be Don Knotts (!!!) who doesn't even have a motive. This one's a little more daring than the film we eventually got (there's a scene with Fred and Daphne, who have adjoining rooms at the hotel, in which Fred tries to convince Daphne to have sex with him). Unlike the Titley draft, which was an ode to Scooby Doo written with a lot of love by an obvious Scooby lover, this script is more like an adult parody/satire of Scooby Doo (but not too adult). It's certainly darker in tone than the Titley draft. Compared to the finished film, this script looks only half-baked (it's only the first draft after all).