I'd never heard of Jonathon Coulton so I looked him up. And, yep, Glee used his interpretation of the song. It's not the first time they've used someone else's version of a song. It's actually common practice. Not just on Glee, but everywhere. From a legal point of view, the copyright goes to the people who initially wrote Baby Got Back. From an ethical point of view...Different story.
Look, if I could speak to Mr. Coulton right now here's what I could say. You've just been given a massive shout out by an extremely popular show. Glee has increased the record sales of Katy Perry, Rhianna, F.U.N., One Direction, etc. You could spend your energy getting angry and fighting them OR you can spend the same amount of energy to find a way to use this.
You can't buy this amount of PR. Glee probably did you a favour by not saying "Hey everyone, here's the Jonathon Coulton version of this song. Just think about how many people are interested in this now because of the controversy. Many more people know about you now than before Glee. Most artists would kill for that level of exposure.
I understand the ego. They took something that's yours and made it their own...which is exactly what you did with Sir Mix-a-Lot's song. You paid money to use the lyrics. They paid by spending millions of dollars to create a music video for your song that is airing all over the world. People are STILL tweeting about it today, long after the show aire.
I fail to see how you lose here.
Post by Johnathon Coulton on Baby Got Back and Glee