I replay 3D more often. I honestly have trouble with the 2D games and therefore don't play them much (Before you say it: Yes, I know I suck at gaming). I probably replay Oot and SS the most, just because I really like them.
I dunno, I replayed alttp and LA several times, maybe the original LoZ as well recently, only OoT and WW come to mind that I replay so much, the rest if the 3D games, not so much.
I find myself replaying the 3D games more often. I guess a big contributor to this fact is the amount of times I've replayed Ocarina of Time, of which I've lost count. Of course, I still love the 2D titles and enjoy replaying them as well.
I don't think I replay either style more often than the other, although I have played Twilight Princess and Skyward Sword more often than all the other games.
I replay 3D games more often. I've lost count of how many times I've played Ocarina of Time and I haven't really replayed any 2D Zelda games yet. I do like the 2D Zelda games, but I find myself playing the 3D ones more. I've also only recently played some of the 2D games.