For me it's a tie between TP, BOTW (haven't played but love her design), and HW, although I could do without the latter's exposed thighs. If you're gonna put her in armour, do it right.
Skyward Sword has a great art style but the Zelda in that game just looks like a regular person. It's like they combined small-town girl character (Ilia/Malon) with Zelda and called it a day.
Although it's among the worst Zelda games, Spirit Tracks will always remain my favorite representation of Zelda. She has more personality than any other version, in her dialogue, actions and facial expressions.
Honestly, I'd love to see another Zelda game with her having this scale of presence in the game. I think that played a big part in resulting in Zelda being so utterly awesome in Spirit Tracks.
Hell, maybe that'd be something they can do in a BotW sequel. Didn't Aonuma talk about the idea of doing co-op gameplay in the next entry? That'd be a cool way to do it- have one person playing as Link and the other as Zelda as they work together on a new adventure.