Amazon thinks you should be protected from GLTB novels
I got this from rydra_wong here:

Amazon is stripping the sales ranks from GLBT books, thus preventing them from showing up in some bestseller lists and searches (and potentially directly damaging their sales), on the grounds that they are "adult" material.

(This is regardless of whether they contain any explicit sex. Meanwhile, books with explicit heterosexual sex scenes retain their sales rank, as long as they're not overtly marketed as "erotica".)

More details here

ETA:
A petition
Twitter - #amazonfail
Roundup Post, includes posts linking to what books are losing their sales ratings.
Contact Amazon's exec customer service dept at ecr@amazon.com to let them know what you think. Customer service phone number is 1-800-201-7575

From arionhunter in the comments, FYI: Not only LGBT books are going under - feminist and general sexuality books are having their ranks stripped as well. Oh, those silly disabled people, trying to be intimate like the rest of us.

[I own that book linked. It's one of the few books that explicitly talks about sex for PWD and includes sections on kink.]

ETA 2:

Amazon Blames Glitch, blah blah. The PW site went down about five minutes after it hit twitter, so here is the text:

Amazon Says Glitch to Blame for "New" Adult Policy
By Rachel Deahl & Jim Milliot -- Publishers Weekly, 4/12/2009 5:49:00 PM

A groundswell of outrage, concern and confusion sprang up over the weekend, largely via Twitter, in response to what authors and others believed was a decision by Amazon to remove adult titles from its sales ranking. On Sunday evening, however, an Amazon spokesperson said that a glitch had occurred in its sales ranking feature that was in the process of being fixed. The spokesperson added that there was no new adult policy.

For most of the weekend on Twitter, in conversations with the hash tag "#amazonfail," users were discussing the fact that the e-tailer was removing the sales rankings for books that it deemed featured "adult content." Many readers, and writers, decried the fact that Amazon appears to be removing the sales ranking for titles that feature gay and lesbian characters and/or themes.

The director of the Erotic Authors Association, who goes by the pen name Erastes, told PW that many of her members "noticed their titles had been stripped of their sales rankings" on Amazon. One, Mark Probst, contacted a customer service representative at Amazon and wrote about the exchange on his blog. Probst wrote that the Amazon rep responded to his inquiry by saying that "'adult' material" is being excluded from appearing in "some searches and best seller lists" as a "consideration of our entire customer base."

Whether a glitch or new policy, titles like James Baldwin's Giovanni's Room and Annie Proulx's Brokeback Mountain are among the titles who have lost their ranking.

ETA 3:
I shoulda been a better OP and been posting updates as they came in.

This started in February

This is not a Glitch

Bantown theory [I don't buy this theory, but YMMV]

Dear Author does a timeline

Dear Author explains metatagging [This is the theory I buy]

Troll claims responsibility [Which I really don't buy, because a) It's Weev and b) it's been debunked. And c) because it only works if you think the only books targetted are GLTB books, and it wasn't.

Debunking of Troll-code