I've made it official CEA policy that we always use lower case. (Edit: If you see "Effective Altruism" on one of our posts or websites in a place where it shouldn't be capitalized, please let me know so I can fix it.)

My reasoning:

1. Like others have said here, I think of EA as a philosophy/system of thought, along the lines of "liberalism" or "utilitarianism", rather than as a formalized religion or political institution, like "Christianity" or "the Democratic Party".
2. I agree that there are specific values and practices that are inherent to EA, but it's difficult to point to any one thing that would "qualify" a person or organization as officially being "part of EA" vs. not.
   1. There is such a thing as a "registered Democrat", but "registered EA community member" isn't really a thing. You can set up a profile on the EA Hub, but so can literally anyone; this doesn't confer any official privileges.
   2. See why I don't like the term "effective altruist" (including my reply to Michael Aird's comment, which pulls out the difference between that question and the capitalization question).
3. Regarding institutions, I consider many organizations to be some degree of "EA-aligned" even if they have nothing whatsoever to do with our movement. I think of this alignment as a spectrum, rather than a binary thing where an org does or doesn't "count".
   1. For example, consider a global health charity that gets serious consideration from GiveWell but doesn't quite pass the bar to be a "Standout Charity". Do the charity's employees have "EA jobs"?
      1. Their work is aligned with EA's mission, and presumably involves what most people in EA would consider a "promising cause area". Given this, I see the "EA jobs" question as beside the point.

In your example, of the person who uses Charity Navigator, I still think the binary distinction isn't helpful:

• Is this person trying to do more good? Yes.
• Is the strategy they're using likely to help them do substantially more good than they would otherwise? Probably not.
• Is their personal philosophy generally in line with EA? Impossible to tell from this single statement.
• Would they fit in well at an EA meetup? Depends on how open they are to considering different ideas.
• Should they be hired for a role at a very EA-aligned organization? Depends on their skills and other elements of fit; their confusion about overhead is just one small fact about them. I wouldn't want them writing curricula about effective giving, but they might be a great accountant.

...and so on.

***

I got off-topic at the end there, but to return to my main point: 

I think that capitalizing "effective altruism" makes it seem more like a binary thing (you count or you don't, you have this identity or you don't) and less like a spectrum (many people are aligned with EA to some degree, but no one is a perfect exemplar of every EA principle). But given how complicated the above questions can get, I think "spectrum" is a better fit than "binary".

I only capitalise it when referring to organisations that have effective altruism in the name (e.g. "Effective Altruism Australia") – i.e. as a proper noun. I don't capitalise it when referring to the philosophy and social movement (similar to feminism, environmentalism etc).

This is also our brand guidelines at GWWC and EAA.

I pretty much echo everything Aaron G said but in short it comes down to the impression left on the reader. "Effective Altruism" looks like a group one could try to join; "effective altruism" looks like a field of study or a topic of discussion. I think the latter is more the impression we want to cultivate. Remember the first rule of EA: WE ARE NOT A CULT!

I generally don't capitalize "effective altruism" just as I wouldn't capitalize "liberalism" or "socialism" so... ¯\_(ツ)_/¯

the community, yes. the practice / approach, no.

I've seen a mix of some people capitalizing effective altruism, maybe more often in communications with a more general audience, and some people not capitalizing it. I generally try leave it uncapitalized, following CEA policy, but sometimes I capitalize it when it makes it clearer that effective altruism is an actual Thing, not just altruism that is effective, and not a generic made-up compound term like, say, "efficient humanitarianism" or "impactful lovingkindness". For example, if I write in a self-introduction "I'm passionate about effective altruism", lowercase effective altruism doesn't read like a term that you could google, at least to someone who has never heard of effective altruism before, so I would probably capitalize effective altruism here. If it's in a context where it's clear to the readers that effective altruism is a specific thing, I would leave it lowercase. Minor note: somehow, some Hack4Impact folks have described Effective Altruism as an organization, in some Slack messages and in a social impact talk they wrote, and capitalizing the term may have contributed to that misconception.