I'm not going to pick a best in this one (unless all the games I'm about to mention get votes) but I can tell you what the worst one is..
Mario Kart Wii. It's the same art as the box, the same art as the game box, and the same art as the title screen, so you get tired of seeing it before you even play the game. The only good thing about it: They are apprently in karts, as we are not seeing their shadows on the ground, but kart shadows.. and they seem to be wearing their wrist straps properly too, so they don't accidently fling their steering wheel through the tv and injure you.
Now, best boxes.. where to being? M&LSS, Yoshi's Island, Mario Party 8, New SMB, SMB, SMB2, SMB3, SMW, SMK, Mario All*Stars, Mario RPG, Paper Marios (that's plural!), Mario Party.. there are just too many to mention, really.
Also, I nominate best/worst caslte/Bowser music.