Episode 45, Inuyasha's second full youkai transformation.

Sesshoumaru's theme starts playing full blast as he rushes forward to attack Inuyasha, but then stops, and Inuyasha sorta sits down all dark-looking, and then the wind changes
exactly when he looks up and you can see he's transformed again...
holy shit. It gave me chills. It gave my
chills chills. And the music was just perfect for it.
Another scene I liked was his third transformation (what is it with these scenes getting the best music?) in episode 52, when he and Miroku were imprisoned by Gatenmaru and "Henkashita Inuyasha" from OST 2 plays. Was that track written expressly for that scene? Because it fit
so well... maximum creepy-coolness.
Others...
Episode 27 - "Dai Hangeki" from OST 1 plays during the battle against the false water kami. I've always loved this battle, and I've always suspected that the reason for that is the way the music goes along with it. (Especially when Inuyasha pulls out Tetsusiaga and slices the guy... I'm always like,
"YEAH, INUYASHA! KICK HIS ASS!!!" XD)
Episode 50 - "Ten Kakeru Sango" from OST 2, when Sango is fighting Kohaku. I think this was the first time this music played, and this one scene convinced me to buy OST 2 (the first one I got).
Episode 118 - Sango's theme ("Sango to Miroku", OST 3), as she swears to Miroku that she won't leave him and that they'll die together. So beautiful...
Episode 124 - "Kusen" from OST 3, when Hakureizan starts to collapse. What I love is when it gets toward the end and Naraku's theme pops up for just a few seconds, as Naraku confronts Kikyou with the wind blowing around all dramatic-like. Soooo cool. *_*
Episode 132 - "Sango to Miroku" again, but this time Miroku's theme (which, incidentally, is pwnage incarnate). When he faces off against Sango, just as the sun is rising all dramatically in the background, and he keeps pressing on even though she seems to have a never-ending supply of things to cut him with. XD I never get tired of watching this scene. Ever.