Of the games in the list, it's a toss-up between Super Metroid and LttP. As with poll #4, I'm giving my vote to Super Metroid just because Zelda is too over-represented.
Personally, I've never considered Zelda my favorite series. Not even close. I don't have the massive nostalgia for it like many do, and I haven't even played every game in the series. To keep it as short as possible, I really enjoyed LttP. It's the best 2D action-adventure game ever, a crowning achievement of the 16-bit era, and it expands on and perfects the 2D Zelda formula to such an extent that it's hard to go back and play the original, which now seems like a very rough, basic prototype (I feel much the same in regards to Super Metroid vs the original Metroid). LttP is longer than the norm for games of its era, but was long enough to feel like a proper adventure and short enough to where I feel I can replay it regularly without having to invest too much time.
But OoT did not click with me back when it was a new game in 1998, a problem I had with the vast majority of early 3D games. I can't remember why, exactly. Maybe it was the controls or the visuals or just the changes made to facilitate 3D gameplay. But for whatever reason, I wasn't impressed like the critics were (though I've been meaning to giving it a second chance, and I really should pick up the 3DS version sometime soon). Because of my feelings towards OoT, as well as other factors, I wouldn't bother with another Zelda game until Wind Waker HD for the Wii U, and I also bought BotW. Both are pretty good, but they have issues that keep them from being worthy of being included in my personal top 20 list, though they'd probably qualify for the 21-50 range of the top 50.