The lead-in to the theme tune in the episode "25", which was helped by brilliant cinematography. Bartlet finds out that Zoey has been kidnapped and he immediately drops the photos of her he's been sorting and his glass of scotch. He then glances at Abbey, and as the background music crescendos, the camera zooms in on one of the pictures. The entire sequence takes twenty seconds, but it's a brilliant 20 seconds.
The use of Massive Attack's "Angel" at the end of "Commencement". It's the perfect balance of creepy, tense and trippy as Zoey realises she's been drugged and then her Secret Service detail realise she's missing, and the repetition of "Love you, love you, love you" as Amy questions Donna's feelings for Josh.
The scene in "Noel" where Stanley pushes Josh to tell him how he really cut his hand and it's shown that music is making him relive the shooting. It's an amazing scene, if more than a little heartbreaking, and the music that helps make it so great?