I know you've probably been asked this a million times, but I genuinely want to know.

My favourite would probably be The Master from Fallout 1, because he thought he was doing the right thing, while the enclave and such are quite obviously evil, im hoping in fallout 4 there's a morally grey area between The Instititute and The Railroad and we get to choose between the 2 sides and have them both play as kinda antagonists.

The Antagonizer. I don't know why, I just like her.

The Legion because they have no corruption,greed and are loyal to Caesar.
Unlike the NCR, they protect caravans for free.

Frank Horrigan hands down, seriously that guy is all kinds of screwed up.

Benny....mostly because he is voiced by Mathew Perry and i didn't even notice.....also because he's actually pretty clever untill he the day i found him again

its hard for me to even call any one a bad guy in the fallout game if you really think about it. I think caesar has a pretty interesting reason for why he established such an old school style army and society. You can even talk philosophy with him in his tent a bit so i suppose he is my favorite. Ulysses trys to be a deep character but for me fails because hes really cryptic and doesnt make a whole lot of sense in the bigger picture

The Special Operative agent, Frank Horrigan

Frank Horrigan, he is a badass supermutant, secret service, killing machine, in power armor.