I've got a bunch of old song demos that sound quite different from the final studio versions, but I'm not sure that's what you mean. The same goes for live versions.

I don't have many examples of songs that have been released more than once on a studio CD. The first one I thought of was The Arcade Fire's No Cars Go, which was one of my favourite songs from their self-titled EP until they revived it for Neon Bible and made it even better. Another old song that benefitted from a makeover would be Interpol's A Time To Be So Small. The old vocal effects were, to be honest, kind of annoying, so the cleaned up version is much better to listen to.