I rooted for Doomsday in the Death of Superman. I Like supes but I just LOVED seeing him get messed up by D-day! 
 
Also Galactus (whoever he's against!) He's the coolest villain ever... a force of nature! 
 
Cheered for Vader all through Star Wars (I'd love to have an empire of my own) 
 
And totally backed Sylar in Heroes against Peter!

Personally I like the heroes better, Green Lantern, the Avengers, Spider-Man.
But I have favorite villains, but I don't root for them to succeed ever.  I root for Superman, because the heroes represent the good that everyone wants to aspire to, or that we hope is within everyone.  And, in my opinion, when the villain is done realistically his or her motivations come from a reasonable place and not from pure evil.  Even Galactus wanted to use his powers for good, but his hunger was so strong he decided to help the universe after he ate.

 
I root for every Superman villain in hopes that they might finally kill him (and he won't come back to life). 
 
And Deadpool, Taskmaster, Carnage, Two-face, and petty much every other awesome villain

Does Jason Voorhees count because I always rooted for him.

I've been rooting for villains since I was...basically 3. They're always the most interesting, have the most depth and psychology, etc, I've always preferred the bad guy.

I always root for Deathstroke, Doom, Larfleeze, Atrocious, Sinestro, andThe Rogues
 
I was rooting for Zod in War of the Supermen as well I was rooting for the evil Teen Titans from the future

dark avengers !!

Lex Luthor, Deadpool, and Darth Vader.

i remenber that in killing joke i always wanted the joker to win over batman 

X- Men 2 and 3: Magneto and Mystique own
 
Jet Li - The One : Yu Law should of won!
 
X-men Origins Wolverine: BarakaPool because Wolverine deserved that beating..
 
Spider-man 2: Doc Ock rules
 

da JOKER !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! :D

Currently, I'm routing for Hiro Kala in his crusade to destroy half the universe lol

I have always loved Magneto... I know some writers have really really bad depictions of him, but I never really viewed him as a total villain...
 
One total bad ass entity that I have always rooted for and always gets excited to see is Apocalypse... 
 
Another one is the Magus! :)

I routinely root for: 
 
-Atrocitus 
-Sinestro  
-Hank Henshaw 
-Captain Cold

It's true that an interesting villain can make a comic book better. Sometimes I wonder what would be like if the bad guys win.

" In the comics, it has to be Dr Doom! Don't know why but I always seem to be cheering for him!  The most recent time was in that movie 'Law Abiding Citizen' I so wanted Gerard Butler's character to get away with it in the end! "

In Utopia I really wanted Norman to put a bullet in Cyclops' head

I root for Atrocitus, I want him to burn Sinestro, Hal, Cyborg Superman and the Manhunters and the Guardians, BURN THEM ALL!!! 

Hmm...I can't really recall if I've ever rooted for the villain, but I know I must've...

If  Marv is a bad guy then I'm on the wrong side of this argument anyway.  Also, I woot for Apocalypse .

Mr. Freeze on BTAS.
 
And Sinestro now and again.  Especially when he's baiting Hal and Carol.
 
I'm not sure Marv is the "bad guy" of the Sin City story, if only because the guys he fights are as bad/worse.  It is easier if you're counting bad guy vs. bad guy stories.  For example, any time Joker has ever encountered a more powerful villain, I'm always pulling for him.

Any villain that wants to kill Hal Jordan I stand behind.

Hold on, are you saying that MAX Punisher is a bad guy? Take a look at the people he's killing. Good and Bad are all relative, so it would make more sense to me, to say Antagonist instead of bad guy. 
 
I root for Dr.light.

@Tom Pinchuk  Thanos during the Infinity Gauntlet and Dr. Doom during Secret Wars

I gotta root Magneto
and when I'm watching wrestling...Randy Orton

i cant help but root for the hood when he is in a comic he is just awsome  
 
and light from death note 

"If  Marv is a bad guy then I'm on the wrong side of this argument anyway.  Also, I woot for Apocalypse ."

@Tom Pinchuk Oh! and how could I forget Juggernaut and Bane!

Infinity War. I wanted Thanos to kick some arse

I've always loved the Thunderbolts and Suicide Squad is without a doubt one of my favorite concepts in comics

" Only time I have ever rooted for the bad guys was when I watched some any gundam series from the Universal Century. I always wanted Zeon to beat the Federation. "