sedo.com is fairly well recognized within the industry, but I believe all they appraise is the domain.
I know when I went to sell wowcensus.com I simply tallied about how long I intended to keep the site running (I hated working on the site - so when the domain expired, I was done) and the average of my AdSense revenue (you could use your own revenue) over that amount of time. I then added in the cost of hosting and domain, and what I would charge someone if I had made that site for them ($25 / hr).
So, essentially, a good formula that worked for me was:
(Avg. revenue per day * # of days remaining in business life) + (Cost to start business) + (Cost, in relation to time, to create website)
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