Preface: TV Specials are counted except Hollywood, Behind the Scenes, The SD Project, Night of the Living Doo and Arabian Nights, as they are just really made to sell the brand name and made as jokes. Video games aren't counted, though I could potentially add them. Most are just randomly placed, though they can't occur during the age of Scrappy-Doo, as he's rarely present. Oh, and the shitty Puppet show and the stage shows aren't counted, because no one should have to suffer through them.
Scooby-Doo Mystery Incorporated is the starting point.
Due to the ending in which the universe is reset, we go from there. The gang is now used to both magic and fake monsters, so pretty unafraid of that shit. Time is reset to be placed earlier, about 30 years, to explain technology.
A Pup Named Scooby-Doo is retroactively added to their memory, as a way to justify their love of mysteries without their selves being aware they lived their lives already. Due to it being added by artificial means, they reference technology in APNSD that wouldn't be present in Where Are You? It's just a remnant of MI timeline.
After that, we go Where Are You?, The Scooby-Doo Show, both iterations of Scooby-Doo and Scrappy-Doo, with The New Scooby-Doo films taking place randomly throughout. They don't matter to story, so they can go anywhere.
13 ghosts takes place after all of those, once the gang are older, in their mid twenties.
Boo Brothers, Ghoul School and Reluctant Werewolf occur back-to-back, placed after 13 Ghosts. This assumes the 13 Ghosts are captured, as the show was cancelled prematurely.
Shaggy and Scooby get their memories fucked with after those 3 successive encounters with ghouls, and can't recall their adventures.
Zombie Island, Witch's Ghost, Alien Invaders and Cyber Chase now take place. In order, they are done Cyber Chase, Zombie Island, Witch's Ghost then Alien Invaders.
Due to the Alien's interference, the group get, once again, fucked over in the timeline. Time is now closer to original Mystery Incorporated timeline. This is pretty much just the Aliens seeing the problem and trying to restore it back to MI, but failing somewhat.
From there, What's New, Scooby-Doo takes place. Then, all the DTV films starting with Legend of the Vampire. There's a soft reboot in terms of personality and appearance, but I wouldn't look into it too much, as nothing important is changed. These DTVs take place in order, in two groups. Everything from Music of the Vampire to Chill Out can go in any order, then Goblin King to current DTVs in any order. The DTV Specials, like Spooky Games and Beach Beastie, are alongside the DTV films, and can be placed anywhere. They can be placed in either group of the new DTVs, post 2003.
LEGO shorts and the LEGO film are just LEGO interpretations of normal adventures. Any order.
Now, this leaves only 6 items unaccounted for: The 2 theatrical films, the 2 DTV films, Shaggy and Scooby-Doo Get A Clue and Be Cool, Scooby-Doo.
The films aren't set in the realm of the animated series, as there are core differences in the dynamic of the gang, and there are references to their past which can't be fixed by any of the animated shit.
Live-action order is simple enough: The Mystery Begins, Curse of the Lake Monster, Scooby-Doo (Spooky Island film), then Monsters Unleashed.
Get A Clue and Be Cool are, without a doubt, the worst animated series. Get A Clue is so stupid in it's premise, that if it didn't include the other 3 members of the gang making cameos, I'd write it off completely. If I had to place it, I'd put it after Be Cool, but before What's New. The gang have a mini break-up after starting college, Scooby and Shaggy do memes with the crazy uncle, which explains why the others only briefly appear, they are busy at school.
Be Cool is irredeemable, but if it must be placed, I'd place it before everything else in the modern timeline, before What's New Scooby-Doo, as they have graduated college by that point, but Be Cool mentions they haven't started college yet.