The Great:
-Loki-This almost isn't fair to the other villains, because we've gotten three movies worth of Loki (with a fourth one on the way) to really flesh out his personality (which is complex). And of course Tom Hiddleston is brilliant in the role.
The Good/Decent:
-Alexander Pierce-Robert Redford brings an element of class/gravitas to all of his roles, and this was no exception. I love how low key he places Pierce, he acts more like the villain in a serious political thriller/conspiracy film than a cackling comic book one. Plus bonus points for being able to convince Robert freaking Redford to say "Hail HYDRA," WOW was that awesome.
-Obadiah Stane/Iron Monger-Jeff Bridges plays him well, his plan is pretty good, and Bridges is so good that he (like Redford) almost make you buy that they're nice guys for much of the film (so it's believable that people would be fooled by them). He only gets knocked points because he turns into a more cackling super-villain giving cliché "evil speeches" during the climax, which was disappointing somewhat.
-Emil Blonsky/Abomination-Tim Roth is really good and the angle that they go with him (old soldier wanting to hang on and becoming addicted to the power that he receives, a drug addict so to speak) was interesting. Plus that fight with Hulk at the end was badass. I'm still hoping that we'll see more of him at some points (especially since they finally brought back ex-General Ross for CW).
-Ultron-Yes, I think that he's underrated. He's not really the Ultron from the comics, but he's interesting nonetheless, and James Spader is great. He's like an angry kid lashing out at "daddy," Tony Stark, and the world, which is an interesting idea at least.
The Meh:
-Ivan Vanko/Whiplash-Mickey Rourke is good, he looks cool, he's got a decent backstory, and they do a pretty good job of building him up as a threat in the first half of the film. But then he spends pretty much the entire second act/into the third stuck in a lab, the focus shifts to the far less interesting Hammer, and then he gets taken out after one of the most underwhelming "final boss" fights ever. Wasted potential.
-Justin Hammer-Sam Rockwell is entertaining, but the character is a joke. The focus should have stayed on Whiplash, the far more interesting character imo.
-Ronan the Accuser-Lee Pace is fun, and I found the idea that, in a movie where pretty much every other character was kind of doing things half tongue-in-cheek, that this guy was super-serious and treated everything that came out of his mouth as the most epic important thing in the history of forever, to be kind of amusing. But he's kind of dull and generic overall, with dull and generic motivations.
-Johann Schmidt/Red Skull-Hugo Weaving is ok, but he doesn't get enough screentime, they don't let him be really evil enough, and Red Skull never really comes across as Cap's archenemy/ideological and philosophical opposite in the film. He feels more like just another baddie that Cap needed to stop, nothing more.
-Helmut Zemo-I found him to be, again, well-acted. But he was a pretty underwhelming villain with underwhelming/generic motivations, and I would have much preferred a more accurate version to the comics (he's both more fun and more interesting there imo).
-Dr. Aldrich Killian-Again generic motivations, and not particular interesting. Stane and Hammer already did most of his schtick, and did it better. And yet again, another "generic white guy scientist/businessman in a suit with a grudge," way to think outside the box there Shane Black. Sir Ben Kingsley was far more menacing and interesting when he was pretending to be the villain than Guy Pearce was when he actually was one. Heck if there needed to be a "twist," then Maya Hansen turning out to be the main villain would have been far more interesting, and unexpected, imo.
The Bad:
-Malekith the Accursed-He's just boring and forgettable in everyway, and a complete wasted of Christopher Eccleston's talents.
-Darren Cross/Yellowjacket-Corey Stoll does his best, but Cross is so generically two-dimensional "evil/crazy," that it's also a waste of a great actor.
NOTE: I'm only counting the main movie villains because, while the TV shows have done a much better job in this area imo, the film division seems loathe to even acknowledge the TV side's existence at all.