It's a fascinating question, and very difficult to answer conclusively (probably partially subjective). Hence my slowness to reply -- busy! But I wanted to run through your list, minus the ones I know nothing about. Numbered lines here are quotes from the first post; in too much a hurry to use quote tags or marks.
1. The Joker
Joker's a tricky thing, because as someone only vaguely aware of him until the recent movie reboots, he's always struck me as perhaps the worst villain of all time due to sheer cheesiness (and he often seems REALLY easy to put out of commision, it's just because Batman oddly never seems to recognize that mass murderer = justified to execute that he sticks around, as I understand it -- that said, the Toa did that once or twice with Teridax too, though, but never really in a situation where it was clear execution was better). And while the new movie made him seem to be a good villain, I wouldn't go so far as to put him near the top of any list. If anything it just made it all the more obvious that Batman should have killed him.
2. Loki from The Avengers movie
He worked surprisingly well. Teridax definitely has a more imposing personality, though. Loki seems very immature... and it works in part because of this, ironically. It wouldn't with Teridax IMO.
8. The Red Skull
Eh, he's fairly stereotypical. He doesn't seem comparable to Teridax, who was a mastermind. (At least according to the movie...)
10. The Green Goblin
I guess it depends on if he's been portrayed better in other media besides the previous major movie series (like the new movie... lol) -- like with the Joker and many of these examples. So my answer is tentative... but all that was really memorable about him from the previous movie series to me was stereotypical evil-ness (not that stereotypical in this case is bad per se, just not "best villain" material), and he looked cool on his hovering green thingamabob. I don't recall seeming unusually impressed by him as I have been for Makuta.
11. Doctor Octopus
I would have to agree here. The Doc Ock movie (in previous series... the second movie, I think?) was one of my favorite movies and I'd watch that obsessively for a while. To be fair, it was more for the magnetic-imploding mini-sun than D'ock himself, but he was pretty good too. But then, in the end he was less a villain and more a tragically mind-controlled previous-villain. Teridax beats him by far in the category of "way too far gone" by the end. Though I do like villains that do that, like Darth Vader.
Maybe it's the Transformers part of this, but no matter how cool the special effects in the movies make him seem, I can't help but just think of him as Stereotypical kiddy villain. Wouldn't want to live in the same universe with him, but in terms of entertainment quality, I think he's just barely par really. (As far as I can tell.)
19. Von Nebula from the Hero Factory franchise (my guess is that Von Nebula could also be the mysterious villain who is behind the events in the Breakout and Brain Attack events)
Er... IMO no... There were moments where it seemed they were working up to this... But then they did invisible-glass-sided tunnel "black hole". Huge missed opportunity, methinks -- imagine what he could be if he really wielded realistic black hole effects and slaughtered thousands in pursuit of his cause -- and once you fall in, without some incredibly advanced (and highly adrenaline-pumping!) tech to counteract it, you be deyehd. I do suspect you're right about the parenthetical statement, but that only proves he's an arch-villain, not a good or near-best arch-villain or villain in general. Contrast to the Makuta who was already pretty mysterious at the start, then really proved himself in the MNOG end, and continued reinventing himself in very good ways all the way to the end.
20. Jafar from Disney
Jafar was pretty great. I'd have to agree.
21. Captain Hook from Disney
Bad memory seems to remember him somewhat fondly from as a very young kid, but compared to Teridax? Nah, he's more just cheesy.
25. Darth Vader
Very yes. Except for "Nooooooooo!" lol
I even like his prequel portrayals more than a lot of vocal complainers. Vader versus Makuta... Hmmmmmmmm.... That's a tough one.
26. Darth Sidious from the Star Wars franchise
Very yes yes yes. Although he's so awesome in a way that seems almost completely unique that it's almost an unfair comparison. I'm especially thinking of the few times in Clone Wars (BTW, it's on Netflix now -- MUST WATCH -- don't believe the complainers; I did and put it off but once I started, it's awesome.... aaanywho) where he fights, and cackles like an immature little kid, far more immature than Loki or just about any other villain, and yet somehow as a Sith it works perfectly, because it's not half-hearted "okay maybe he's a little immature", it's "his vision of the Sith is pure unashamed immaturity and selfishness tempered perfectly by the most advanced strategy, so he's like the worst schoolyard bully you can imagine times a thousand." And he's pretty great in the movies too. Although IMO he's had to be a bit rehabilitated by the prequels and Clone Wars and I guess other media from the original trilogy. He featured so little in the first three it was hard to tell this about him, though it was there.
Comparing to Teridax, I think they're both pretty equal in terms of mastermind-ness. It's proven directly a lot more often with Sidious in the Clone Wars and prequel movies, though; with Teridax there are a few key proofs that the authors could write him as a mastermind, but with Sidious there are countless impressive examples if you pay close attention. But this is less about the character and more about length of story and interpretation really. And of course, Teridax was only vaguely hinted at that his future goal MIGHT include conquering a galaxy; Sidious actually did it. What they did conquer, though, they both did through misdirection as much or more than direct conflict; brains over brawn.
I think Sidious has one clear thing over Terry too -- in his "end" (I've heard it wasn't final, but that's not my point here), that was when his personality and philosophy really emerged front-and-center (in the original trilogy). With Teridax, it emerged in the takeover and moments soon after, but after that point, it was fairly detached, and his end has winnage because giant robot battle, more so than anything unique to Teridax as a character. (I'm obviously seeking to overcome this in my version. ) On the other hand, Teridax has a fairly unique tragic reveal at this time that I think still puts him up there on the list, that he was supposed to take over all along and might have actually gotten to keep the body if he had stayed good.