I mostly recommend Link's Awakening, with Minish Cap in second. Those two were the best, in my opinion. But, that's also just my opinion, it really depends on what you want out of a game.
Minish Cap does have better graphics and is all-around much more colourful, but Link's Awakening has more of an emotional impact and dungeons that require more thinking overall, as well as being more difficult. MC also has more of a connected overworld, whereas
LA does sometimes feel a bit more disjointed due to everything being placed on a grid.
To me,
LA really is better, although MC is much more colourful and, uhhh, kinda more modern, if that's your thing.