One interesting case is Iceman. In most of the animated adaptions he's portrayed as an only child, but in Spider-Man & His Amazing Friends he had a half-sister and in X2 he had a little brother.
Kitty Pryde's also an only child, I believe.
Sonic the Hedgehog, Tails, and pretty much everyone in the Sat AM series were only children as far as I know (unless new silbings popped up in the comic that I'm not aware of)
Kit Cloudkicker (Talespin) can be assumed to be an only child, being orphaned and all.
The Mystery Inc gang (Minus Shaggy & Scooby) were all only children. I don't recall ever seeing siblings for Fred, Daphne, Velma, Scrappy, or Flim Flam.