The feather or leaf are obvious ones if we're talking about one dominating an entire title, but the galaxy games did such an amazing job of actually designing levels around a power-up that if I had to pick one I've most enjoyed in the past, it'd definitely be the cloud.
3D Land and 3D World did a really good job with their power-ups as well. Sort of like the 2D games but much better balanced than any of them.
edit: also, I'm surprised NSMBWii isn't getting better representation in here. It was the only NEW title to do power-ups well. Propeller, penguin, and ice flower are all fun (even if the last two are a little repetitive). It also made good use of the fire flower in some levels, and it used the mini mushroom at least as well as DS ever did. I think it's actually a better balance than any other 2D game struck, besides maybe SMW. The DS had atrocitites like the Shell power-up, 2 was generic as all hell, and the squirrel suit in U was just...boring. Mega Mushroom was pretty fun at times though. Wouldn't hate seeing that again.