Juggernaut - Dude is just fun to read when written right. He isn't trying to really kill people or take over the world he is just trying to get a goal done and make money.
Bane - I love his back story
Dr. Doom - Depending on circumstances.
Loki - Most of the time he's just playing a game.
Honestly most of the time it depends on the motivations of the villains at the time as to whether I root for them or not.
If the stakes aren't very high and I think the hero could use a good loss I'll root for the Villain only if I think they are cool.
Also I've never rooted for Magneto to win mostly because at the end of the day his way of doing things involves killing a lot of innocent people so at that point and time he has no more justification for his actions imo.
I don't think you could consider Magneto a true villain since the 1970's, really. He's had so many layers added to his character since. He's not really a hero, but he's an important leader of mutantkind. Grant Morrison tried to return him back to hard villain days (though he was influenced by Sublime), but thankfully that was retconned.
Lex Luthor is interesting, in that he could be one of the great leaders of humankind - if only Superman hadn't come to Metropolis and inadvertently taken the spotlight from him.
I found myself rooting for Mr. Gone when reading The Maxx.
When I used to read the Larry Hama Wolverine's, I found myself cheering for Cyber because he was just insane to me. He was hilarious and I thought it was so badass when he broke wolverine's claws off.
I absolutely cheered for Thanos during Infinity Gauntlet, and he wasn't an anti-hero at that point in time.
I honestly can't say I really root for any villains of DC, unless you count Black Adam. MAYBE Sinestro, but I don't really know if I root for him, I just like his character. It's not like I want him to win or anything. There's never been a point in time where I was like "You know what? I think Joker should win this time."
The only thing I CAN say is that I sometimes ADMIRE the badguy's brilliant plans, like Luthor in 52; but I don't really root for them.