I can answer the first part of the question, but I'll save Lord of the Flies for someone else.
First, did you see the movie? *The fact that you asked the question suggests maybe you didn't, or at least not all of it. Anyway, I'm going to spoil the end. Also, if you DID see the movie and if you liked it (I loved it), the book is great also.
The most obvious answer to the Appearance vs. Reality question in Fight Club is the fact that throughout the story Brad Pit and Edward Norton appear to be two entirely different characters - leading lives that each envies of the other. As it turns out, they are the same person. The main character suffers from insomnia and this plays out by his experiencing two completely separate personalities.
Another one is the idea of the fight club itself. It might appear to be something dangerous, illegal, and possibly just silly/stupid - to an outsider - but for the men involved, it is life-changing. The rules "never talk about fight club" enhances this life-changing aura it carries. These men start to see each other in the day - noticing black eyes and bloody knuckles, and it gives them a sense of comaraderie and pride. They beat each other to pulps, then hug and act like best friends. It is a twisted display of testosterone and desperation - and somehow, it is endearing.