The music in the beginning of Half Blood Prince when the Death Eaters fly through London and destroy Diagon Alley along with Millennium Bridge, as well as the music in the slow-motion scene of the photographers taking all the pictures of Harry and Dumbledore. Later on in the film, the panning shot over Hogwarts to Draco in the tower as it snows outside is great, and so is the music at the very end when the trio look out from the tower into the sunset.
The music that plays as the Trio break the chains off the dragon they got away from Gringotts on and fly off like they (and the dragon) just found freedom.
Alexandre Desplat's score for Deathly Hallows Part 1 has some fantastic moments as well. The music at the very beginning when Hermione erases her parents' memories of her is heartbreaking, and really captures the feel of that scene, impressing upon the audience that this the beginning of the end of the series. The music when we open to Malfoy Manor is very sinister, and the music when just Harry and Hermione are in Godric's Hollow is unlike much of the other music in the series... Desplat uses Spanish guitar. And it is beautiful. Oh, and the music when Bellatrix throws the knife at Dobby as he proceeds to Apparate himself, Harry, and Hermione out of Malfoy Manor, which results in his death upon arrival at the beach is dripping with anticipation.
If you thought the score for the first film was good, Alexandre Desplat outdid himself in Part 2. Just listen to the "The Tunnel", music matching the fast-paced ride through Gringotts, and especially"Statues" and "Courtyard Apocalypse", similar heartbreaking songs used during the Battle of Hogwarts.
"Lily's Theme". Almost silent, and still epic. Portraits perfectly the beginning of the very end of the series. It screams "It's almost over now..."
Outside of scores, though, the Weird Sisters' music is great, "Magic Works" being a perfect slow dance song that sounds like something out of a John Hughes movie from The Eighties.
"Journey To The Cave". Just this bombastic piece as Harry and Dumbledore arrive at Voldemort's Horcrux cave.
"Dumbledore's Farewell". It's from Half-Blood Prince, but is also used in the scene where Harry views Snape's memories in the Pensieve. It's heartbreakingly beautiful.
Patrick Doyle's music for the Quidditch World Cup opening. It goes from a light Irish-sounding tune and moves to a men's choir.
Nicholas Hooper created some amazing music found in a deleted scene from Half-Blood Prince.
For the most epic piece of music to come out of the franchise, we have to look somewhere beyond the films: the license game version of Order of the Phoenix's "Dumbledore and Voldemort" by James Hannigan. The awesome riff is also found in "Wand Combat".
Another powerful piece, "Procession", is heard in the end-half of Deathly Hallows Part 2 when Voldemort is returning to Hogwarts' courtyard with his remaining followers and Hagrid, who is carrying a seemingly dead Harry. The atmosphere just gives out utter sorrow and hopelessness after the fatal battle.