Actually, Final Fantasy 6 IS on Virtual Console. It's just called "Final Fantasy 3". The actual second and third installments of the series weren't released in the US way back in the day (Square of America believed they were "too complicated" for American audiences). So when they originally released 4 and 6 (and not 5 for the same reason), they were released as Final Fantasy 2 and 3 respectively. It wasn't until Final Fantasy 7 came out that people in America realized they'd been gypped of SEVERAL installments in the series, and it would still be a few years after that before we saw the actual installments and the correct numbering.
So, FF6 is there. They probably just legally HAVE to call in FF3 when referring to the US SNES release because that IS what it was called at the time. But I think it even admits in the description that there was a naming error and that it is actually FF6.
As for Earthbound, the whole reason they claim they won't re-release in Virtual Console is that one of the battle themes sounds a lot like an actual song, so they're just trying to avoid copyright infringement. This is Nintendo's actual story. I call BS though. I mean, it WASN'T infringement years ago in its original release, so why is it now? Furthermore, the track is only played TWICE in the whole game. If they're so afraid of using the track, would it be SO hard for them to substitute it with another one? Hell, I'd play those two fights in silence if it's what it took; that song being there - while cool - just isn't that important to me.
Finally, Mother 3 PROBABLY didn't see US release because of Nintendo of America strict censorship policies. That doesn't make it okay, but I do get it. In a lot of censored games, they get around things by fixing little details here and there or changing the word ever so slightly. But there is actually a fair bit of (tactfully written) homosexual innuendo and humor, a (very clever concept of a) race of "genderless beings" that look like drag queens, and an entire (brilliant) dungeon that revolves around a drug trip. Of course, I only speak for myself, but none of these things bothered me. The story is one of the best to be in a JRPG in almost ever, the game is a blast, and if they had to slap a "T" or even an "M" rating on the cover just to get it over here, fine; it wouldn't change my thoughts (or most peoples'). But, Nintendo would just rather... not.
And this has been my long trivia rant from "Lynn: The girl who knows too much about video games". I hope I didn't bore you too much. ^_^