Full disclosure - Surgo and I are bureaucrats (sort of a super admin, mediawiki has weird access level names) at dnd-wiki.org, and responsible for a lot of the policy there. I'm trying to keep that from biasing the following.
Why Are There 3 Wikis?
Internet history time!
Back in 08 or 09 (it was before my wiki time and forever ago by any internet measure anyway), the only homebrew wiki was dandwiki.com. There were a bunch of admins and regulars there who were tired of arguments over balance, tired of unfinished cruft, and generally wanted to clean up the wiki. They began discussing instituting a quality control and review board (in retrospect the review board was a terrible idea on a volunteer board, but that's a story for later) and came up with a plan for doing that. Since there was general wiki agreement and no actual wiki opposition they went ahead with the changes one night and updated policies and whatnot. Note that I'm not actually sure if the majority of the discussion occurred off wiki in an irc chat, which would have been bad form and partially responsible for the next part.
The owner of dandwiki.com, who goes by the handle of Green Dragon there, wasn't as on-board with the changes as it had appeared, and sort of flipped the fuck out. What followed was a policy edit war and a whole bunch of bans handed out by the owner to his admins for their trying to update the policy over his reverts. And then an admin banned the owner, who unbanned himself and banned/demoted every admin on the site. It took a couple of days to cool off, during which time the admins and regulars involved decided to just leave. Everyone who migrated took their material and reposted it to a new wiki, dungeons.wikia.com.
I came on board shortly after the fork to Dungeons @ Wikia, and did enough stuff for the site in the background and policies that I was made an admin. About a year after we started there Wikia decided that they wanted to embrace casual and mobile in a very direct way and drastically change their look (anyone who was with wikia 3ish years ago may remember this change; it's when the WoW Wiki forked as well). That meant discontinuing support for our preferred wiki skin and a bunch of features that we were making quite a bit of use of, and also locking article width to a pixel maximum. Which pretty much killed it for us, because it meant a massive rethink of the layout of our nav and everything with a large table on it (classes) and everything with an author box on it (almost everything at all) and we had just finished getting it to work and rebuilt from the first move. We got our own domain and some server space, and so we moved again. Wikia still hasn't restored the functionality that it had before we moved, making it hard to navigate except through google or internal search, but licensing and policy prevent us from purging it more thoroughly. We won't be talking about wikia from here out.
The new, new place was dnd-wiki.org (which is annoying because of confusion with the dandwiki), and has been working out for the last 3+ years now. About a year and a half ago the owner of the dndwiki.com domain offered to point it at our servers, and so we got a second domain name. I prefer the .org address because we have more direct control over it, but they're both fine.
So yea, 3 homebrew wikis out there. To summarize:
[*]dandwiki.com is the original DnD homebrew wiki.
[*]dungeons.wikia.com is a fork of that, and has been largely abandoned (also, they never did fix their navigation).
[*]dnd-wiki.org and dndwiki.com point to the same homebrew wiki, which is separate from dandwiki.
Ok, history out of the way, there are some rather serious differences between dandwiki and dnd-wiki.
On IP Edits
dandwiki.com decided a long time ago (or the owner decided for them, I'm not actually clear on that) that they wanted to be a "wikipedia like wiki". Which meant incremental updates to all of the articles by whoever wanted to make them, as well as retaining incomplete pages that still had potential future value. In order to make that easier they went and removed their author displays and protections, so the only way you can see who wrote an article is to check the page history. And if you want your article to remain as you wrote it (or at least vet any potential changes), you have to use the 'notify on change' wiki feature and then go double check it. There is no policy about respecting authorial intent, since the stated goal is incremental improvement. An example consequence of this policy is that the Kantian Paladin listed there is not the same Kantian Paladin listed in the community tome bits, and is actually a pile of half-casting progression ass.
dnd-wiki.org also allows IP edits, but did not remove the author displays or protections. One of the fields in the author display is a set of editing rules, that indicate which sorts of edits are allowed (generally only grammar and clarity, but individual authors can specify whatever they want). It is specifically against policy to edit in violation of those guidelines, and other policies are designed to respect the intent of the original author at all times. There is an active group of editors who enforce that policy, and revert edits from IPs or registered users that violate these rules, and repeated offenses can result in bans. It's a wiki though, and things can slip through.
On Marking Homebrew
There have been a few threads in various non-Den places about how the articles on the wikis confuse casual users about what's SRD and what's homebrew. We don't really care much here though, but it has larger community use implications. It really wasn't well marked in either place though, and so the criticism applied to both wikis to some degree.
Since dandwiki removed their author displays, there wasn't anything separating a homebrew article from an SRD article or a OGL article. A user was working on getting it displayed, and and had a text header on some pages for a while. According to the user the site's owner removed the displays, despite initially agreeing to them. I can't be bothered to verify that account, but it's pretty clear that the displays were never adopted more broadly and can't be found now.
Dnd-wiki.org had author displays on all of the homebrew pages (because they care about authorial control), but decided that it wasn't sufficiently obvious (because internet people are lazy). So they made a graphic for it and added it to their author display. It now shows on every page that is homebrew, right above the author and editing information. It looks like this:

On Quality Control
I don't think anyone here would really dispute that there are different things against which you could balance your material. It's really hard to talk about article quality with respect to balance when you don't specify a desired balance. As Tome games are quite clear about, over or underpowered options are relative to your companions and the challenges you're expected to face.
You do not specify a balance on dandwiki.com. They have a "not balanced" tag, and balance is part of the article rating that they have, but the guidelines are largely missing. Some people balance against JaronK's tiers, some balance against the SRD, some balance against more esoteric bits and they're all basically accepted because 'who knows'. There are user ratings that you can place on the talk page, but they don't appear on the article page unless manually added (the rating system has been in discussions for revision as recently as a year ago, and might be removed entirely in the future). Additionally, there is no cost or benefit to having a low or high rating. There is a single (and infrequently updated) featured article slot on the main page, but it's filled with a nomination and voting process completely separate from the rating thing. This ties in with the owner's position of wanting to retain and improve incomplete articles to create a sea of articles with different intended balance and degrees of completion.
dnd-wiki.org uses a set of balance tags originally defined with the SGT and requires a declared balance goal on most article pages (races and gear are excluded, as our balance ranges don't make sense for them). You can tell if an article is supposed to be over- or under-powered for games that you would want to use it in at a glance, assuming you understand what the balance ranges represent. There are user ratings as well, which can be added from the article page and a summation of them appears on the article page under the author information. Actual ratings text is restricted to the talk page. An article must have a certain number of positive ratings to be eligible for rotation in the community favorites slots on the main page (there are several articles in random rotation), and a certain number of negative ratings will cause the article to be removed from navigation until identified concerns are addressed. Older articles are less likely to have these ratings because they're a newer system though, because volunteer community and whatnot. dnd-wiki.org also deletes incomplete articles if not finished or actively worked on for a period of time (as well as complete articles on author request). So article cruft is largely eliminated and crap that remains can be sorted by consensus.
Hopefully this text wall has been helpful and I can just link people to it the next time anyone gets ???s about a wiki.
If you care about helping a wiki get a search leg up, link to the one you like and ignore the ones you don't. If you're doing a google/bing/whatever search for stuff, that might mean looking through the results a bit until you find the one you care about.
More informations:
[*]Original dndwiki thread
[*]Discussion of initial blowup and dungeons @ wikia fork
[*]More dungeons @ wikia discussion (and then 4e class design and Frank's Baneguard)
[*]Notice of dnd-wiki.org fork