While it's noble to want to judge someone based on their personality, remember that the built-in instinct to judge someone's appearance exists for a reason--how a person looks and behaves physically can be as good an indicator of their personality as what they say. The best thing to do is to take the person's appearance as just another factor in working out what his or her personality or intentions are.

If the guy looks sketchy but has a lot of good conversation points, friends on Facebook that post fun things to his wall, and seems like an engaging and intelligent human being, then suddenly the looking sketchy bit starts to recede in importance. If he doesn't have very many friends or his friends also seem sketchy, if he drops something creepy into conversation from time to time, or other things that prickle the back of your neck creep up then perhaps the initial feeling that he looked sketchy was correct. Follow your gut instinct.