And the Valkyria no Bouken series by Namco on the NES/PC-Engine, and a handful of decent PS1 clones...
I tried not too long ago Goof Troop and wasn't disappointed

It's a far-from complete list: any feedback would be welcome. I'm trying to put together lists for Smash Bros-like games, Dragon Quest-like games, and possibly more..
I realize I didn't answer the question.
My first experience with the series was the epic Zelda III (and it has a semi-sequel for the BS-X, "Ancient Stone Tablets", too!) and then Minish Cap and all three Gameboy Color offerings, my judgement may be blinded with nostalgia, but they're all good.
At the time I played the hell out of the DS games and used to be drolling over Wind Waker until I got it in 2009, but I wouldn't go so far to say they're the best Zelda games out there.
The 3D ones... I'd say a tie between Ocarina of Time/Majora Mask (a mission pack that manages to one-up the original, like with Tengai Makyou Kabuki Den) and Twilight Princess. Loved Skyward Sword, but it was too linear/short.
Wind Waker, Phantom Hourglass, and Four Swords (both GBA and GC games) were disappointing though. Zelda II is a whole different thing. Didn't play the 3DS game yet, so I can't say anything about it.
Marvelous on the Super Famicom was Eiji's Aonuma first game. It ran on the Zelda III engine. And it has now a fan-translation for the main game (but not the two episodic spin-offs). By all means, go and try that one out!