The best fight in Naxxramas is Thaddius.
There are so many reasons this fight is great. First is the atmosphere. It's all about constructs and electricity, strongly evoking Frankenstein's Monster. Polarity, splitting into two, positive and negative, so much great flavor. The layout of the room even reminds me of a MOSFET.
Second is the introduction to the fight with Stalagg and Fuegen. It's beautifully designed to split your raid in half, allowing a seamless transition to Thaddius. Simultaneous kills are always a fun mechanic. The swapping of tanks is hilarious. It reinforces the whole shifting sides flavor of the fight.
Third is the jump to Thaddius' ledge. Why is there a jump? There doesn't need to be one. But it's there, and it's just a little bit of extra challenge. It's also something that lends itself to memorable fights. A lot of people talk about the jump and it probably generates more chatter than any of the other elements.
Fourth is the polarity shift mechanic on Thaddius himself. I just find watching for polarity shifts and running around Thaddius to be fun. It's a mechanic that also beautifully reinforces the primary flavor theme of the fight.
Lastly, I really like the strategies available to defeat Thaddius. I've only killed him with the two-point strategy. But the four-point strategy is elegant. It's one of the few strategies that have really impressed me with its cleverness.
(Four-point is to form a square around Thaddius with the two groups on diagonally opposite points. On a polarity shift, if your charge changes, run to the point on your right. If your charge stays the same, run to the point on your left.)
Thaddius is the best fight in Naxxramas. It has great flavor, and elegant mechanics which serve to strongly reinforce that flavor, while still providing a challenge for the raid.