A list of religions, plus the options 'none' (for atheists and agnostics), 'no preference' (for those who don't know/care), 'none of the above' (perhaps with a 'please specifiy' text box in case it's satanism or something).
How many people would understand the difference between "none" and "no preference?" How many would just select both when doing their searches? I'm willing to bet a beer per question (more actually, since there's no way I can think of to test this- so bet heavily) that the answers are "not many" and "most if not all."
I'm not sure if I've seen "None of the Above," though I have seen "Other." But just as you, an atheist (right?) see a big distinction between "agnostic" and "atheist" and "no religion," plenty of people with religion see those as all the same thing, but wish there were more options for "Southern Baptist," "Old School Southern Baptist," "Whatever sub branch of subbranch." Unless you're running a site aimed at free-thinkers (or whatever you want to call a group that will mostly self-identify as agnostic or atheist), this approach is not likely to help.
If it was to be a list of religious philosophies, or attitudes towards religion (in which atheism would properly belong), it would have to be something like:
Atheist
Agnostic
Believer in single deity
Believer in multiple deities
etc
Again, unless you're buiding skeptidate.com, this approach is not so helpful. "Believer in single diety" encompasses all forms of Xianity (or at least, it can, depending on how you view the trinity thing), all forms of Islam, all forms of Judaism, Zoroastrianism and probably a bunch of smaller religions that don't fall under this rubric. This doesn't tend compatibility.
The multi-god option will get Hindus matched with wiccans and with assorted animist religions.
If the question is 'Religion?' then the atheists answer is 'none'. If you ask an atheist what their religion is, they will tell you they don't have one. They won't say 'my religion is atheism'.
But you might say "I'm an atheist." Match.com bundles the whole thing under "faith." Is that any better?
But, to take you literally, If I were building a dating site, I wouldn't have a list at all, I'd have 'soft' personality questions like "is religion important to you?" and "do you believe in an afterlife?"
Again, unless you are building a site for a skeptic-type market (and I suppose that's a fair answer to the question I asked- it just means I asked the question poorly), this is no good. For one, people are going to search on their overall religion (and then on importance, I think), not on issues of the afterlife or the divinity of Christ or biblical inerrancy. The details will come out later.
Remember that the goal of the site is not to provide perfect descriptions of people, but rather to get reasonable descriptions that include the quantifiable things most people ask about. The next step is taking all those quantifiable, searchable things and getting them searched.
Given that the thing has to be searchable and has to appeal to the general public (which in this case is made up mostly of people with at least a little bit of religion), how would you phrase the question so that it A) met your standards/needs for describing you accurately and B) met the needs of the general populace, for whom the different denominations of Xianity are of great importance and the issue of whether atheism is a religion is of little no importance?