I feel like the NTSC box art is usually lacking in comparison to its Japanese counterparts, however, there are a few I enjoy.
I'm selecting only handheld box art because it is my favorite (announcing my bias right now) because I prefer handhelds and also because I find the dimensions of the box themselves to be very aesthetically pleasing when you have them lined up on a shelf. Yes, it is as superficial as it sounds, but that's just my tastes.
Anyway, I'm a fan of the Link's Awakening box. It's simple, clean, but the shield and title look very crisp against the plain background.
I also like The Minish Cap box for similar reasons. It's very simplistic in design, but very forthcoming with details specific to the game (such as the kinstone behind Link and Ezlo pictured).