I'd valuate a site based on how much the site earns annually - which means total income minus total expenses. But you may also add the value of the site's other assets.
Re other assets: a site may earn $x a year net, but the site may have other assets that contribute to its valuation. Most of the time, that's not a factor. Sometimes it is.
For instance, owning licensing & publication rights to a site's branding or content can be worth $, if&when the content is republished as a book, turned into a movie, spawns a line of snowboarder fashions, or whatever.
case in point [imdb.com].
When someone tells you the value of their site, be sure to find out what that number really means. And if you're selling, you may show them a really large number, but you must (ethically) also communicate clearly to the buyer what that number means.