Specifically, villains from the original "Scooby Doo, Where Are You?" series of 1969-1970. For starters, the top 10:

The Alien ("Kooky Space Kook")
With his hulking, spacesuited form, pulsating glow, hideous skull face, and inhuman laugh he is one of the scariest and certainly most original Scooby villains ever. He also has that great ghostly spacecraft and its sound effects. Best of all, he is handled right. The pacing and timing of his appearances is perfect, and he is treated as a serious threat throughout. Ironically you realize at the end that he's never actually DONE anything except walk around and look menacing. But he does that so well!

The Phantom Shadows ("A Night of Fright is No Delight")
Visually they are interesting variations on the traditional shrouded ghost. They are also among the few Scooby ghosts to actually show seemingly ghostly powers onscreen. They appear to float, they have those horibble moans, and you can even see through them at times (An effect that's never explained, by the way). They are also handled well. Memorable ghosts that any ghost-hunter would be proud to meet.

The Witch and Zombie ("Which Witch is Which?")
The witch is another villain who actually seems to do something supernatural onscreen. She floats in the air, appears and disappears in a puff of smoke, makes Daphne vanish, and is shown (in flashback) conjuring the zombie from the flames. For his part, the zombie makes a good henchman. With her magical know-how and his brawn, they make a dangerous combination.

The Castle Ghost ("Hassle in the Castle")
His simple sheeted shroud wins no points for originality, but he's actually one of the more impressive ghosts. He floats in the air, is transparent, walks through walls, and has a great spooky laugh. In shots where his face approaches the viewer the looming eye-holes of his head remind one unpleasantly of the sockets of a skull. It goes to show that poor episodes can have good villains.

The Ghost of Hyde ("Nowhere to Hyde")
He never actually speaks, but his character design, animation, and volcanic laugh (courtesy of John Stephenson, the underrated voice actor who played so many Scooby villains) give him lots of personality. He also gets several good scenes, including a couple of effective shock moments.

The Backstage Phantom ("Backstage Rage")
Though he's much too camera-shy in the first half of the episode, he makes up for it in the second half with several chillingly memorable scenes. The shot where Scooby suddenly sees him silently gazing at him from across the room is an all-time spooky Scooby highlight.

The Galloping Ghosts ("A Gaggle of Galloping Ghosts")
Individually these three--a fruity-voiced vampire, a lumbering Frankenstein's monster, and a snarling wolfman--are common monster-movie cliches. But together they make a veritable army of spooks. Throughout the episode you never know which one will pop up next. They're all the more impressive when you finally learn at the end who they are.

Captain Cutler ("A Clue for Scooby Doo")
Captain Cutler's glowing, seaweed-draped hard-hat diving suit makes him a visually impressive character. He also has a wonderful first appearance. But then...nothing, until a couple of brief appearances late in the day. It's a sad waste of what could have been an absolutely first-rate ghost.

Elias Kingston ("What the Hex Going On")
Easily the most malevolent and scary Scooby ghost, he scares you in the first scene with nothing more than his sepulchral voice intoned over nightmarish imagery. Indeed, that's his problem--he's really TOO scary for Scooby Doo and has to be toned down later in the episode.

Charlie the Robot ("Foul Play at Funland")
With Charlie the animators took the trouble to give him a distinctively, unnaturally precise walk. This plus his glowing eyes and odd musical cue make him an effectively weird, seemingly otherworldly character. The only problem is he turns out to be very far-fetched even by Scooby standards.

What's a fruity voiced vampire?

Next, some mid-level monsters:

Redbeard ("Go Away Ghost Ship")
Redbeard is one of the most vivid characters, with his booming voice (again courtesy of John Stephenson) and the cheefully malevolent way he keeps hinting at the unmentionable. Unfortunately he doesn't have any truly good individual scenes, he's saddled with a pair of complete ciphers for henchmen, and his episode is not a very good one overall. It's a shame--he could have been a contender.

The Headless Specter ("Haunted House Hang-Up")
More wasted potential here. The Headless Specter has a brilliantly effective introductory scene. And he's one of the most inherently creepy Scooby villains. Unfortunately once the gang actually meets him the whole thing turns into farce. The ensuing silly chase scenes work well enough, but they represent a letdown after the careful buildup of menace in the first half of the show.

The Mummy ("Scooby Doo and a Mummy Too")
From here on there are lots of rather two-dimensional, lumbering, inarticulate menaces. The Mummy is one of the better representatives of the breed. He's not very original-looking, but he makes an effective heavy. He's strong, inexorable, and has a knack for appearing when you don't expect him. This last saves him from mediocrity.

Tzen Tuo and the Zombies ("Mystery Mask Mix-Up")
Tzen Tuo himself is a bit of a let-down. He's extremely bombastic, nowhere near as cool a character as he obviously thinks he is. His zombie henchmen save the day with a couple of quite effective creepy scenes. And there's that great chase scene where we learn that some zombies can actually drive cars!

The Snow Ghost ("That Snow Ghost")
The Yeti-like Snow Ghost is another not too ghostly ghost (apart from the scene where he seems to fly). His greatest distinction is the fact that he is the most vicious of all Scooby villains. He tries to saw Velma in two lengthwise, nearly blows her and Scooby up with dynamite, and attempts to hurl Scooby off a cliff. Shaggy is lucky that when he fell into the beast's clutches he wasn't "turned into a ghost" sure enough!

The Black Knight ("What a Night for a Knight")
It's interesting that this excellent pilot episode--moody, atmospheric, with plenty of beautiful visuals--has a rather run-of-the-mill villain. The Black Knight is a fairly good-looking ghost, but he never does anything ghostly. He just lumbers around like an old-fashioned guy in an ape suit. He's really nothing more than a serviceable menace, for an episode that fortunately has a lot of other things going for it.

The Creeper ("Jeepers it's the Creeper")
Not much of a character, really. He's just an ugly-looking guy who runs around chasing people. We're told he is "a phantom who can walk through walls" but are never shown anything like this. The Creeper's one redeeming virtue is that he's game for anything (We even see him riding a horse at one point!) and makes a good patsy in an episode that puts extra emphasis on slapstick.

The Ghost Clown ("Bedlam Under the Big Top")
Some might rank the Ghost Clown higher due to his effective air of quiet malevolence and his impressive hypnotic abilities. Those hypnotic abilities are part of the problem--he's too much like a comic-book supervillain for comfort. More seriously, this guy proves creepy in more ways than one in his treatment of the only female character to fall into his clutches.

And now, the real losers:

The Indian Ghosts ("Decoy for a Dognapper")
Still more wasted potential. The ghostly Medicine Man is a fairly good-looking ghost who gets a couple of reasonably effective scare scenes. That is, they could have been effective IF the viewer hadn't already been introduced to him before the Meddling Kids meet him in a scene that makes it clear he is merely a flesh-and-blood crook. The apparition of a galloping Indian brave that appears is a dandy, but we don't see it until half-way through, and then just before the above-mentioned scene spoils it. It's a real disaster.

The Werewolf ("Who's Afraid of the Big Bad Werewolf?")
Here's another example of a good episode that lacks a truly good villain. The Werewolf is a run-of-the-mill concept that has nothing very original done with him. But what really undoes him is the way Shaggy and Scooby repeatedly make a complete fool of him. And he just lets them do it! When the Scooby villains all meet in prison he must be the most humiliated guy in the bunch.

The Witch Doctor ("A Tiki Scare is No Fair")
The Witch Doctor looks okay, but has no really good scenes. He also turns out to be a fraidy-cat, literally panicking at the sight of his own reflection! He at least has a good henchman in the form of the gloriously absurd semi-robotic Mano Tiki Tia.

The Caveman ("Scooby's Night With a Frozen Fright")
He runs around, he grunts, he hits things with his club. And that's it. About as mediocre as they come. He does have the honor of being the first ever to say "And I'd have gotten away with it too, if it hadn't been for these meddling kids and their dog!"

The Ape Man ("Never Ape an Ape Man")
In his first appearance the Ape Man engages in actual hand-to-paw combat with Scooby--and loses! From then on he spends as much time being chased by our heroes as he does chasing them. He is undone by a simple trick that sends him sliding helplessly across the floor, wailing for help. What a loser!

The Miner Forty-Niner ("Mine Your Own Business")
He's not really very scary looking. He never does anything ghostly. We hardly even see him MOVE. The Miner is a complete cipher. The episode's few good moments owe nothing to him.

The Wax Phantom ("Don't Fool With a Phantom")
What appears to have been an attempt at a different design flops with this lumpy, nondescript humanoid. He doesn't do anything ghostly, has no good scenes, and has some rather embarrassing ones, notably when we see him run through a brick wall in a gag that belongs in a Roadrunner cartoon rather than a Scooby adventure.

Charlie the Robot is probably my favorite of the Scooby Doo Monsters, but oddly, I don't remember much about the episode.

The image I now have in my head of all these characters in prison stripes standing around complaining about Scooby and the gang is priceless. Thanks, Daphne.

I love this thread. Thread, where have you been all my life?

In the second movie, you see all the old villains, at a bar. With Wack-a-scoob games.

Maybe "Coolville" has its own equivalent of Arkham Asylum for incarcerating Scooby villains. 'Cause you've got to wonder whether some of these guys were in their right minds to pull some of the stuff they did....

Reminds me of a panel in a 1970s "Flash" comic in which a bunch of his foes were standing around using a dummy of the Flash for a dartboard. Something very Silver Age about that.