I think the Lawbringer perk would have worked better if 'evil' was otherwise worded as 'outlaws'. As far as the fingers, I thought similar to what bonustime said, that the individual wanted the fingers to put through some sort of fingerprinting device. Where this doesn't make sense is that raiders, etc. born outside of civilization may not have any kinds of records, though, are we sure this even pertains to raiders, or just bosses considered 'evil'? If you give the fingers to a scientist, you could always imagine, as also stated above, that he can read something from the blood involving aggression.
As for the 'Solar Powered' perk; I didn't think it was SO dumb only because I could imagine if you had been living in the wastes for sometime and developed a mutation, you could simply be absorbing the UV radiation from the sun, in turn helping along your mutation process. Just like when you grew that mutated toe in F2, you didn't have to become a ghoul to do that. I put it along those lines.
Regarding the others, I don't know what's so bad about the few I've seen here, and just because you know how to talk to children (which I suck at in real life) doesn't mean you're a pedo... hmm...
So I agree with Sarfa.
The reputation system is a good idea, but how would you indentify how people react to you, etc. if you didn't call it good, evil, etc.? I mean, even the original games had some labels like that, like champion when you were the good guy, or whatever it was for the bad. (I just remember the image of the guy with the black mustache and top hat)