The core DND 3.5 rules do not cover physical attractiveness having fallen back to just using the Charisma attribute as first used in the 1st edition of ADND. And in that time period of the late 70s several variants were offered; one that comes to mind is the Face and Voice sub-attribute system. Charisma, being more of a personality based score, did not adequately capture the fact there are very charismatic people who just don't look all that impressive as well as beautiful people with the personality of a rock. With the publication of the 1st edition Unearthed Arcana came the Comeliness score which I will modify for use in my game until something better comes up or the need for attribute disappears.
Comeliness is not Charisma though Charisma affects the Comeliness score.
Of course the old attribute score from 1st edition does not work seamlessly when plugged into a 3.5 game. For us it does not change any of the skill checks or 3.5 rules in any way other than to give an idea, on an admittedly artificial numbering scale, of physical attractiveness. And it must be pointed out that what one race or culture finds attract another does not. For our purposes though we will adhere to a higher ideal of universal beauty.