I tend to root for the bad guys. First of all, for some reason they're always really hot compared to the protagonists lol j k. Also, they tend to be more interesting than some guy waving a weapon around yelling about "Justice will prevail!!" and "I'll protect the world from evil!!!!!". The villains tend to have more depth to their character (unless it's like a shitty gag manga). They usually have a reason for being evil, and some kind of deep angst-y side to them, that you can't help but falling for. They're more interesting than some generic idiot who tries to save the world from evil.
I would say evil...but there are some that have their own reason to do things that just tend to go against what others believe is just...for example the genei ryodan of hunterxhunter. They don't appear evil, but they do what they must to do things like avenge a fallen person and go so far to put a show. Sometimes people have to die in the way especially when they go after what they need. Like it said they are the reason that this orphan city is still alive because of the money they steal.
Good guys. Bad guys are awesome, but usually I either hate them for doing bad things or feel really, really sorry for them. There is almost nothing sexier than a guy who stands up for what is right AND kicks butt at the same time.
in manga I usually like the villains... but not necesarilly evil... but mostly yes... the only movies where I don't like the villain are star wars... I absolutely hated sidius (although the acting and the was brilliant) I just hate dictators... also vader doesn't count since he turned out to be a good guy... eventually