Like some other people on this thread have said, I care about the personality of the character more than anything else. Typically, I find most characters of both appearances described in this thread to be anything ranging from dull and boring to vulgar and annoying, but certainly not good characters.
However, there are some exceptions to both, for me.
An example of one of the few pretty boy type characters that I like is Kurama from Yu Yu Hakusho. I couldn't care less about his appearance, since its his great wits, and surprisingly complex set of emotions that make him such an intriguin character to me. He never becomes annoyingly whiney or useless, and yet at the same time, he doesn't just magically have a "cool" way to get out of every situation. He is simply just a brilliant "thinker," one who can come up with strategies under all kins of heavy pressure (whether it be for battle or something else important, like when he used to pull off big acts of thievery as Yoko Kurama in Demon World). I could really go on and on about why I like his character, but as anyone would notice, all of my reasons for liking him have to do with what his character is on inside, and how he interacts with other characters, and reacts to certain things and situations. Absolutely none of my reaons for liking him have to do with the qualities and features of his physical appearance, as I honestly couldn't care less about what he looked like, since its what's inside that really counts.
Likewise, for a muscle-bound character, I've always liked Son Goku, even in his adult form in which he is insanely muscular. But that's because, as its obvious to just about anyone who has either seen or read Dragon Ball (or both, of course ), Goku starts out as an innocent and pure-hearted child, both in his outside appearance and on the inside, but when he grows up....he's bascially that same exact likable character, which is why I couldn't care less how insanely muscular he got. No matter what he looked like, he was atill a very appealing character simply because of the great qualities of his simple yet very likable personality and sense of thought (IMO, anyways).
So, even though my answe was very long, I think I clearly demonstrated that the question of whether I prefer a character of a certain appearance over a character of another type of appearance is almost completely pointless, to me, since what they look like is really irrelevant, when it comes down to who they truly are.