I feel that Skyward Sword is definitely the best in the series. OoT is a great game but I didn't love it as much as the other Zelda games. Actually, it feels rather dated playing it. I didn't play it when it first came out, so I don't have any nostalgia with that game (I played TP and WW first). TP was my favorite before as it blew me away at how much Zelda had evolved. Now SS is my favorite.
Skyward Sword's dungeons were much more fun and better designed (OoT's felt rather cut and dry at times).
SS also has a great cast of characters. Groose was a nice surprise. At first, I thought he was just a superficial character who bullies Link. I never knew he would become much more than that, and so likeable too. I also felt SS's story was the best. They did a great job with the storytelling. One of the reasons I couldn't get into OoT as much was its storytelling and characters - the setup was great, but the storytelling was so simple and on the surface, that I couldn't feel much attachment to the characters (WW had better storytelling). Skyward Sword really went further with the storytelling out of all the Zelda games. The characters were so alive, and I was surprised at the emotions I felt in the game. Plus, Zelda played a huge role in this game, and it now makes sense why this game is called "The Legend of Zelda" - a much better reason than the story used in AOL. Out of all the Zelda games, I cared about SS's Zelda the most. And the final boss battle - most epic fight ever.
I had the most fun with Skyward Sword, and it's actually going to be the first 3D Zelda game that I will be replaying immediately. I don't usually replay games when I beat them, even when I like them a lot. But SS was so damn fun that I actually can't wait to replay it.
The only thing I felt SS was weak in was the instrument. Here, I would give it to OoT for having the best use of a musical instrument. I loved SS's soundtrack, but I wished they had done more with the harp, like let me pluck individual strings first to know the basic notes before just strumming.
Overall, SS is legendary. By far the best game with the best storytelling and gameplay in the series. SS took the best parts of each Zelda game in the last 25 years and put them all in one game. It definitely made the biggest emotional impact on me too.