I'll say TP's Master Sword cutscene, because there's a lot of buildup to that moment, with Zant cursing Link and bringing Midna close to death, to meeting with Zelda (not to mention the soundtrack during this section). The cutscene itself is also quite memorable, with the curse on Link breaking in the middle, and even better, Midna is there watching everything unfold right before her eyes!
I have to give honourable mention to OoT's Master Sword cutscene also, not just because of nostalgia, but also because of the guilt you feel afterwards. Well done, Link, you've just unknowingly helped Ganondorf take over Hyrule. Also, adult Link is pretty awesome. Overall, a very memorable cutscene.