Everything about this game was really amazing. It's sound track, as Josh mentioned, is my second favourite right after MM. The Opening Theme, Outset Theme, Legendary Hero, Windfall Theme, Dragon Roost Theme and Farewell Hyrule King are some of the best Zelda themes ever crafted. And they all have such a nice tune. Most of them are very relaxing, such as Outset Theme and Dragon Roost Theme. Others are very epic, like Farewell Hyrule King and Legendary Hero.
The graphics are another huge part of what I love about the game. They are just amazing to look at. Some of the beautiful visuals include looking out across the ocean as the sun rises, seeing Valoo on top of Dragon Roost, and seeing Hyrule Castle for the first time. The graphics just fit so well with the tone of the game, and I love just looking at everything. Especially the way the bombs explode, the way the ocean moves and some of the funny expressions Link has.
The world is also quite amazing. It just seems so... Full. Islands every where, each with treasure charts, heart pieces, upgrades, mini-games, interesting people, towns, dungeons. So many things. I love Windfall Island. Aside from Clock Town in MM, Windfall seems to me to be the most beautiful and complete Town in any Zelda game, and I love how you can decorate it. Outset is also another quite nice town. I love the sequence when you first come back to Outset after getting the bombs, when you come to get Nayru's Pearl. Everyone is just so happy to see Link, especially his Grandma, even though it is so dark and terrible outside.
The Dungeons are very good as well. They always seemed to be very vast and extensive, and always a little difficult, but not to difficult. This was a perfect level for me back then, as this was my first Zelda game. The Dungeons always looked so beautiful, and had very interesting puzzles. Some that stand out to me are the visuals in the Wind Temple, especially that massive room with the big hole and the fan, the Mirror Puzzle in the Earth Temple, the boss of Dragon Roost caverns, and of course Molgera. That was quite an epic boss.
The items in this game, though similar to others were quite amazing. WW introduced the Grappling Hook, which had so many uses, and was always fun to use. The Elemental Arrows were also very cool, even though there are no new ones, they always have interesting uses, and are quite funny to use. Especially the Fire and Ice arrows. The Skull Hammer was one of my favourite items, as it looked so comical for Link to use, but it was just so satisfying to smack a Moblin with one. I always used it in combat. And the late game edition of the Hookshot was also quite welcome.
The second quest was also very nice. I love how you can carry over all of you're hard work in the Nintendo Gallery from the first quest, and now that you have the Deluxe Pictobox at the beginning of the game, you can complete it. I also liked how you could stay in you're pajamas for the second quest, because I always thought they were cute.
And last but not least, the characters are defiantly unforgettable. Such as Tetra, and all of the other pirates, who were always hilarious. How they were so wimpy, and scared of a twelve year old girl. The look on Salvador's face makes me laugh every time, and the guy in the snow suit. (I forget his name) Always trying to do business. I love the expressions on people's faces when you out bid them by 2000 Rupees at the Auction House, and that annoying girl who steals from the shop at night, who you get to hunt down.
All in all, Wind Waker is one of my favourite Zelda games, and is very unique in the way it works, the gameplay and the emotions it gives. It is truly a master piece.