It's not certain exactly which universes the multiple series and movies would take place in. This is an attempt to sort out which shows/movies belong in which universe.
Universe 1: It’s safe to say that Scooby-Doo, Where Are You!, The New Scooby-Doo Movies, and The Scooby-Doo Show all exist in this universe. The reasons it’s separated from Universe 2 would most likely apply to the addition of The Scrappy and the regular consistence of the Scooby-Doo Hoax being thrown out. This universe is the most consistent and obvious, as well as being the one that most long-term Scooby-Doo fans are familiar with.
Universe 2: The 1979-85 era of Scooby-Doo, which takes care of all the Scrappy series, and is the one fans would like to be rid of the most. Whether or not you want to split this universe up into two different ones, between the frauds and paranormal is up to you, but there is likely more than one "sub’universe" involved here, containing episodes with the five original gang members, the episodes where they all disappeared, the episodes where Daphne returned, and the movies starring Scooby, Shaggy and Scrappy.
Universe 4: The 2000’s revival of the franchise, placing the gang in the modern universe and causing them to catch on to the constant frauds much quicker. While it mainly applies to What's New, Scooby-Doo?, it’s likely that the Direct-to-Video films from 2002-2009 are also included, for similarities of animation and for placing the gang in the current time period.
Universe 5: The universe that includes the Direct-to-Video films from 2010 and onward. The animation improved, and the continuity between Universe 4 is disrupted in Big Top Scooby-Doo!, where Shaggy states that he does not believe in Australia, despite visiting it in Scooby-Doo and the Legend of the Vampire. Although the animation is similar to that of Scooby-Doo! Mystery Incorporated, the show’s story arc suggests otherwise.
Interesting enough, it was in this universe where the torch for the official voice of Shaggy got passed from the late Casey Kasem to Matthew Lillard.
Universe 6: The live action universe. 'Nuff said.
And some works stand out in their own universes:
Scooby-Doo! Mystery Incorporated: Though after the series finale, the show actually takes place in a second universe, completely destroying the original one. The new universe is implied to be the one from Scooby-Doo, Where Are You!, but since the gang had already unmasked various monsters from that seriesnote Seen at the Crystal Cove Museum, it is likely an altogether new universe.
Of course, it's not hard for the entire franchise (except maybe the live-action stuff) to all take place in the same universe, since the series as a whole has no continuing storyline and the time period is never made specific, other than some of the technology (one of the reasons for the original series' durability is that it WASN'T very time-stamped). Only minor details would have to be explained (most of which can be solved by simply shuffling the order of the shows/movies), and animation style means little, especially when its never been THAT different. It's really not supposed to be thought about very hard, or taken nearly as seriously as something like Star Wars, the DC Universe, or Star Trek. Also, this doesn't even BEGIN to cover media like the chapter books, picture books (several dozen of which have original stories), the long-running comic book series (for almost 20 years), the 70s comic book series, and video games.
The original Scooby-Doo, which debuted in 1969, kept its voice actors throughout the franchise shockingly consistent for a large amount of time. With Casey Kasem voicing Shaggy until 2009, Frank Welker voicing Fred Jones presently, and Don Messick voicing Scooby-Doo up until his retirement in 1996 (he passed away the following year). That being said, Don Messick's death had a strong impact on the series overall. When I say that, I don't mean that it was sad, and the series had to find someone else to voice Scooby; there's more to it than that. Scooby-Doo on Zombie Island was made in memory of Don Messick, and many fans agree that because of this movie, the series was revived in the 2000's, due to the 1990's being a pretty dormant time for Scooby-Doo. It's because of Messick's death and the film being made in memory of someone that the series was revived in the 2000's and is still going on strong to this day. Messick's death may have been the overall contributing factor that led to the creation of Zombie Island, which saved the series' life.