I'm not too sure who is familiar with Web of Trust, so I'll start with a brief description. It's basically a browser app that inserts a circle next to text links in websites. The color of the circle indicates whether or not it's average rating by users rates it as having a "good reputation" (green) or a "bad reputation" (red). There are four criteria: Trustworthiness, Vendor Reliability, Privacy, and Child Safety.
Singularity.org's printout is here. As you may have guessed from the title, Web of Trust lists Singularity.org as "poor" in trustworthiness, vendor reliability, and privacy. There's a comment that, when translated (via Google translate) says "Mass mailing of non-thematic Forums". It's also commented under the category "malicious content/viruses".
I'm not entirely sure how these ratings are generated, (How Ratings Work, related) but I've used it for several years, and this is only the second time I've disagreed with a rating. I've always found WOT to be very reliable, and a decent way of warning me if a site is unsafe so I don't have to think about it. So I was fairly alarmed when I saw the red circle there, since I'd imagine it's turning away people that don't know any better. If LW had a red circle, I never would have come here. I'm not sure what SI or LW can do about it, but there's a "click here if you are the owner of this site" button, although I don't know what that does. I've left my own rating on there, but it didn't seem to change the overall rankings.
Edit: When I made this post, the scorecard read Trustworthiness 30, Vendor Reliability 31, Privacy 31, Child Safety 100.
It's strange. How can you even measure "Vendor Reliability" of every web domain, when many domains don't sell anything! But don't worry, the "global community of millions of users" will assign you the exact value between 0 and 100 anyway. For example "lesswrong.com" has 95, and "singularity.org" has 31 -- I guess some customers were really angry about Friendly AI delivery time.
Despite having four different criteria, the values seem mostly the same, so I guess it's just a "like / dislike" voting. The website refuses to say many people have voted, so it could have been just one or two people who disliked... something.
The FAQ in the site gives some instructions on how to "increase your site's reputation". These include: join the site, and ask your friends and customers to join the site. (And then, presumably, give yourself a high rating. D'oh.) Before you do that, another part of FAQ says that votes from new users have low value, and only increase gradually. So you should use the site a lot, and preferably install their browser plugin. (You can't pay to increase your website's reputation, but free labor is always welcome.)
But the important part is this: Someone from SIAI should follow the link "Click here if you own this site", verify the site ownership, and request a review. They will be probably asked to provide a site description, link to Privacy Policy, and Contacts. This will generate a new topic in the forum, where someone can respond, and also many users will visit the domain and give new ratings, which can fix the bad result if it was caused by only a person or two. (This is my idea from looking at their forum; I haven't tried it.)
The difficult part will probably be to describe the site in a way that doesn't pattern-match to something bad, because I guess most users will just read the description, spend 15 seconds on the site, and enter some ratings. (The users who rate many sites have high weight in the system, so I bet the ones with highest scores don't waste a lot of time before making their judgement.) Especially it is necessary to avoid pattern-matching to scam sites, as those seem to be the greatest concert for WoT users.
EDIT: Maybe we could do some brainstorming. What Bayesian evidence is there to confirm or contradict the suspicion that SIAI is a scam organization? The "singularity" seems not to be a problem, for example "kurzweilai.net", "singularityhub.com" and "singularityu.org" have high ratings.
Done (with at stretch at the "someone from SIAI" part). Comment above