I've seen bits and pieces of the various Scooby series over the years. Perhaps not enough to form the most solid opinions, but my take -
Scooby-Doo, Where Are You! - The one that started it all, and set the general tone for the franchise. While pretty flawed - particularly in the not-so-fleshed-out personalities of Fred, Daphne, and Velma - this series was pretty cool. I liked the dark, foreboding feel brought about by the artwork. Nice "monsters," as well.
The New Scooby-Doo Movies - Already starting to feel a little too whacky. The guest stars don't really add much (although a few of the team-ups - particularly with Batman and Robin - worked). Not to mention the celebrities' presence rarely made any sense. Story lines are needlessly stretched out to 45 minutes.
The Scooby-Doo Show - Admittedly haven't seen much of this one. Looks like a sillier version of the original series. Known for featuring Scooby-Dum, a hillbilly cousin of Scooby's, and Scooby-Dee, a female cousin whom Scooby is apparently in love with (?)
Laff-A-Lympics - May not be considered a true Scooby series. A parody of "The Battle of the Network Stars." It's kind of a shame that the idea wasn't fleshed out a bit more. I can see it working as an extreme precursor to CN's "Total Drama" series. Fun to watch at least an episode or two, but the formula gets old rather quickly. Also, huge script flaw - the Really Rottens regularly lose points for cheating in events, but the other two teams get off scot-free. Shouldn't Babu's Magic be called into question by the judges?
Scooby and Scrappy-Doo (half hour version) - Believe it or not, Scrappy saved Scooby's declining ratings. That being said, I think that the main problem with Scrappy was that he took on the roles already occupied by Fred, Daphne, and Velma, making their inclusion pointless. Otherwise, the idea of an exuberant nephew assuming that his nervous uncle is actually a brave detective is amusing.
Scooby and Scrappy-Doo (seven minute shorts) - Scooby, Shaggy, and Scrappy run away from real monsters, pirates, and smugglers for seven minutes. Not much else happens. Occasionally joining the trio is Yabba-Doo, a Western sheriff uncle. Scrappy and Yabba appeared in a handful of shorts away from Scooby and Shaggy - the only series not to feature any of the original Scooby gang.
The New Scooby and Scrappy-Doo Show/The New Scooby-Doo Mysteries - Daphne's back, and this time has adopted a team mom role. This was likely in response to the lack of stronger female characters in Saturday morning programming. Fred and Velma occasionally appear during the second season, and the mystery element has returned.
The 13 Ghosts of Scooby-Doo - Interesting idea, but not as well executed as it could have been. On the plus side, the writers (led by future Tiny Toons/Animaniacs writer Tom Ruegger) are given small moments of creative freedom, predating A Pup Named Scooby-Doo. One episode doesn't even focus on the series' story arc, but instead on Scooby quitting the group, and being taken to a world in which he was never born. Vincent Price is a nice addition. But the less said about Flim-Flam and those two comic relief ghosts, the better.
A Pup Named Scooby-Doo - The first series to take the Scooby concept and poke fun at it. There's a sense fun and creativity that had been missing from Hanna-Barbera for decades. The use of full animation and wild Tex Avery-style takes is also a welcome addition.
What's New, Scooby-Doo - Haven't seen, but am under the impression that it's Where Are You! for the '00s.
Shaggy and Scooby-Doo Get a Clue! - Haven't seen, but have heard people regard it as the worst Scooby series.
Scooby-Doo - Mystery Incorporated - Have seen a handful of early episodes, and found it to be quite enjoyable. There's a combination of the classic whodunnit elements, character development, clever in-jokes, and a story arc that doesn't feel forced.
Be Cool, Scooby-Doo! - Have heard mixed opinions on it.
Many of the direct-to-video movies seem to be pretty enjoyable. Less so the TV movies - namely Scooby Goes Hollywood and the Superstars 10 entries - and the live-action movies.