This is an interesting topic. Among the many psychological challenges the boys face on the island, appearance represents both the first and last issue to be dealth with by all the boys.
When Ralph is introduced at the outset of Lord of the Flies, he is shown immediately taking off his clothes and luxuriating in the freedom he has discovered in a world without adults. Quickly however, Ralph understands the practicality of keeping his shirt on to avoid sunburn.
As his hair grows out, Ralph grows increasingly frustrated with the obstruction of his vision and the discomfort of having hair in his eyes. Symbolically, we can interpret this discomfort as a preference for civility on Ralph's part. He does not wish to let go of rules, order, and the world of civilization. He wants to be saved.
As Ralph's civilized world disintegrates, Jack's savage society becomes more distinct and powerful.
Jack presents quite the opposite attitude toward being saved (returned to England) and toward his appearance. He is the first boy to hunt and to paint himself in charcoal. The play and freedom available to the boys on the island is overwhelming in its appeal to Jack. He embraces the wildness of a world without rules, ultimately engaging in a man-hunt with an aim to kill Ralph.
Jack's body paint is representative of his complete willingness to eschew rules and order, despite his initial fervor for creating rules that must be followed. Jack does away with the civilized clothing that once distinguished him from the animals and, importantly, from other boys. By painting his face and following the wild laws of nature (hunting and killing), Jack becomes something of an anonymous savage.
Ralph and Jack contrast each other in many ways. Their appearance is just one of several. First, Ralph seems to value his appearance as a decent, well behaved and well dressed schoolboy. Whereas, Jack quickly discards his shirt, thus starting his decline in appearance. As the story progresses Ralph seems to hang on to his pride in appearance possibly as a connection to his civilized nature. Jack digresses in his appearance becoming very savagely dressed. Jack also paints his face possibly in attempt to mask the horrible things he starts to do. So basically, Ralph clings to his civilized appearance while Jack's appearance as well as behavior continue to become more and more uncivilized.