I'd like to start of being say that I find it quite amusing that 9 people voted that they believe Majora will appear again. I'm pretty sure that due to Majora's Mask occuring after Skyward Sword, that Majora wouldn't be able to be killed, which to be honest, doesn't sound that great an idea. I also doubt that Nintendo will use any of the antagonist's that aren't Ganon again, but meh, what do I know?
I believe that either Ganon or a completely new antagonist, not one that has already been used in the past of the Zelda series. I'm leaning more towards a new antagonist appearing in Skyward Sword though, as I find the theory that unless Ocarina of Time is before that game, Ganon cannot appear, very plausile.
I am leaning towards a new antagonist appearing in the series though. I think Nintendo will want to freshen the main platform Zelda games up with a new antagonist, and use the theory that Ganon doesn't appear in the timeline until Ocarina of Time as an explanation for him not being there. I'm hoping for an antagonist that seems like a mad freak, but is actually highly intelligent. Something like
Mayuri Kurotsuchi (I couldn't remember his name, so I had to find any variation of it :xd
.
I don't want to see Ganon appear in the next few main platform consoles for a while, as the only games in which he hasn't been the antagonist that I am aware of, are the games made for the DS.