Well, I won't comment on that since every site has to have its own way to pay the bills.
But another way is subscriptions. I know of one site that has spent the better part of its existence flaming and screaming about anyone who tries to recoup any of their costs through selling software or having subscriptions but has now decided to join reality and is now asking people to give them money.
WinCustomize is light on such things because Stardock funds it from its software sales. Apparently, Jay, pop up ads are better than being funded through software sales as some "elites" feel that Wincustomize isn't a real skin site as a result.
But like I said, bandwidth is expensive so they all have to have some way to generate revenue. Pop up ads pay quite a bit better than banner ads. You won't see them here because they are simply too annoying to deal with.