1.) Ganondorf - I can't honestly say that this final encounter was more epic than OoT. But what I can say is that it is hands-down the most well executed, paced, and designed final battle in any 3D Zelda game. TP was the true homecoming for the series, and having a four-stage fight that pays homage to the best parts of the series was amazing. Possessed Zelda was an amazing "Phantom Ganon" fight with a sick twist on Zelda's Lullaby, Ganon was a great callback to the beast-pig forms of the past, horseback riding with the traditional Light Arrows was amazing and got Zelda into the fight in a believable manner, and the final sword-fight is the closest we've ever gotten to a true one-on-one sword duel. TPHD can really put this over the top for me if it makes it just a little bit harder.
Oh, and the final battle with Ganondorf boss music is one of my favorite themes in the entire series. Probably top 5, honestly.
2.) Stallord - This is a perfect example of a new idea that was implemented in a spectacular fashion. The Spinner in and of itself is an awesome item, but I can see where the challenge came in when it came to actually using it in a boss fight. The solution? Ditch the common conventions of a boss fight entirely and go bold with something new. The result is something that we had never seen before in any capacity, and the "epic scale" gets continually turned up when we start getting higher and higher on the column and Stallord gets whittled down to just his head. It's also super cool that this is our first mirror piece, so the urgency and sense of scale is already higher than it had been in the first three dungeons.
3.) Blizzetta - Her face and the Shadow Temple are the only things that have ever truly scared me in a Zelda game. Just the whole concept of the boss is pretty awesome; she's an innocent soul who just got terrifyingly possessed and looks exactly like a demon from hell. With that aside though, I really like how the Ball and Chain is used in this one. Ice physics keep it from being too easy, and with probably the most epic boss music besides Ganondorf himself, it's a pretty memorable encounter.
4.) Zant - I don't get why people don't like this guy's role in the story. It could have been implemented better sure, but the concept is still neat enough. We have this borderline psychotic man-child who in his darkest hour found a "god" that made him all-poweful. I've always said that more foreshadowing for his true character would have made the reveal better, but I digress. Going through all the boss areas and mechanics we've had beforehand was great, with Zant giving his own crazy twist on them all. Him prancing around like a crazy guy just made it that much better.
5.) Armogohma - It might be the easiest boss in Zelda history, but it's still super fun. The idea of a super-huge terrifying spider is great, but the way that it's taken care of is even better. It's just so satisfying to crush a massive spider with an equally massive fist with an item that was just so weird and cool to use. TP has a problem with cake-walk bosses, but this is the only one where I feel like that factor really holds it back too much.
6.) Argorok - This one gets good points for the atmosphere and build-up it had. Being so high in the clouds for the dungeon was cool enough, but facing off against a good-old traditional fire breathing dragon at absolute maximum altitude was somehow even better. It's too bad that the fight itself is kind of clunky, since the double Clawshots were kind of awkward to use in the first place. I also wish they had done a bit more with his design, since I always thought it was more on the generic side.
7.) Morpheel - Like Argorok, the atmosphere for this is great, but for a different reason. The very, very long and slow trek into a watery abyss does a great job of establishing that "hey..... I'm not going to be able to run from this", as well as just giving the player an uncomfortable feeling just because humans associate deep water with dying/not breathing. The fight itself though it pretty forgettable. It's probably the easiest one in the game, and under-water controls are something that 3D Zelda hasn't really been able to nail yet without a Zora mask.
8.) Diababa - This guy is pretty meh for me, which is understandable since it's the first boss. The design is pretty cool, but the method you use to fight him isn't very fun to me, probably due to the lack of items at that point. Plus I still hate that stupid monkey.
9.) Fyrus - Probably the only boss fight I straight up don't like. It just seems so uninspired and phoned-in. Oh, I hit a shiny eye-like thingy with the bow? Never seen that one before. /sarcasm