Julie Farkas and Arcade Gannon are up there. I don't care what anyone says Preston Garvey and the Minute-Men are one of the most righteous and genuine organizations inn a fallout game and the whole "Another settlement" meme is stupid. You're a group coming together to help those in need, of course another settlement needs you. Raul is rad, no pun intended. Frank Horrigan is badass but the enclave sucks. I don't care for any legionary's they're half-baked and no pros about "Rebuilding civilization" or better trade routes will excuse slavery and the abuse of women. Joshua Graham is interesting though. The NCR sucks too, leave people and their land alone, don't annex their homes and charge them insane taxes. I only recently got a PC so for the first time ill finally be able to play 1 and 2, so i don't really have any favorites from that. Three dog is awesome in that he is doing something to fight against the oppressive thumb of the enclave.
Maybe I'm just too dramatic, but when I'm playing an RPG I am judging characters based on a moral compass over them just being cool. So yea, the Followers, Minute-Men, Riley's Rangers (Though they want compensation), those are like the coolest kind of characters to me.