For the entirety of the 60's
Best Character: Spider-Man. There's really no competition here. Peter is the only one who I thought had meaningful character development, and he's by far the most easily identified with.
Worst Character: Henry Pym. Might as well have named him Blandy McBlanderton for all the development and character he had in the 60's. Single biggest moment for him at this point was the death of that one ant, y'know that one that only appeared in the story it died in and has never been mentioned since.
Best Group: Purely from a character perspective I've gotta go with the Avengers. FF should probably win overall, but in the late 60's the Avengers really turned the character stuff up. The introduction of the Vision and him dealing with the ramifications of his origin, the personal conflict of the Black Panther, and of course Cap adapting to the modern world. All good stuff.
Worst Group: X-Men. This one is just far too obvious. The characters as a whole are entirely bland and uninteresting. Iceman and Angel are both pretty obnoxious, and Cyclops whole "I can't express any feeling because the powers I seem to have perfectly under control might one day be a danger" thing is utterly stupid. And Xavier is a dick.
Best Romantic Subplot: None of these were particularly good IMO, but Thor/Blake/Jane was the one I liked the most. Sure it was predictable, but Jane dreaming of polishing Thor's hammer pretty much makes up for everything else.
Worst Romantic Subplot: Matt/Mike/Foggy/Karen. Matt considered proposing to Karen as Mike, 'nuff said.
Best Villain: Doom is the only one who I though had much in the way of development and character. Plus the dude's just awesome. Special runner up prize for that one guy who impersonated the Thing in what is easily one of my favorite issues in the order yet.
Worst Villain: Mekano! AARGH! Lame villain with lame abilities and the single stupidest motivation for a villain yet. I can't hate this guy enough.