Through Time and Space

Taken from Wikipedia:

Track no. Track Episodes used in
1 "Doctor Who Theme" (TV version) All post-2005 episodes
2 "Westminster Bridge" Rose, New Earth (Variations in The Long Game, The Doctor Dances, Boom Town, The Parting of the Ways, Fear Her)
3 "The Doctor's Theme" Rose, The End of the World, Boom Town, Bad Wolf, The Parting of the Ways, The Christmas Invasion, The Satan Pit, Fear Her (Variations in The Runaway Bride, and in the Torchwood episodes Day One and End of Days)
4 "Cassandra's Waltz" The End of the World, New Earth
5 "Slitheen" Aliens of London, World War Three, Boom Town, Love & Monsters
6 "Father's Day" Father's Day, The Parting of the Ways, Rise of the Cybermen
7 "Rose In Peril" Bad Wolf, The Parting of the Ways, The Impossible Planet
8 "Boom Town Suite" Boom Town
9 "I'm Coming To Get You" The Parting of the Ways
10 "Hologram" The Parting of the Ways
11 "Rose Defeats The Daleks" The Parting of the Ways
12 "Clockwork TARDIS" The End of the World
13 "Harriet Jones, Prime Minister" World War Three, The Christmas Invasion
14 "Rose's Theme" The End of the World, The Parting of the Ways, The Christmas Invasion, New Earth, The Age of Steel, Fear Her (Trailer at end of episode), Doomsday
15 "Song For Ten" (performed by Neil Hannon) Extended version of song used in The Christmas Invasion (originally recorded by Tim Phillips) with additional lyrics (Non-vocal versions in School Reunion, The Idiot's Lantern, Army of Ghosts).
16 "The Face of Boe" New Earth, Gridlock
17 "UNIT" The Christmas Invasion
18 "Seeking The Doctor" Rose, School Reunion, Love & Monsters, Army of Ghosts, (Variation in: The Parting of the Ways)
19 "Madame de Pompadour" The Girl in the Fireplace
20 "Tooth and Claw" Tooth and Claw, (Non-vocal section: The Satan Pit)
21 "The Lone Dalek" Dalek, The Impossible Planet, The Satan Pit, Doomsday
22 "New Adventures" Boom Town, The Parting of the Ways, New Earth, The Satan Pit, Doomsday
23 "Finding Jackie" The Parting of the Ways, The Satan Pit, Love & Monsters
24 "Monster Bossa" Boom Town, Love & Monsters
25 "The Daleks" Dalek, Bad Wolf, The Parting of the Ways, Army of Ghosts, Doomsday, Evolution of the Daleks (discordant note used multiple times in Daleks in Manhattan)
26 "The Cybermen" The Age of Steel, Fear Her (Trailer at end of episode), Army of Ghosts, Doomsday
27 "Doomsday" Doomsday, (Variation in The Runaway Bride), (Vocals Only: Rose)
28 "The Impossible Planet" The Impossible Planet, The Satan Pit
29 "Sycorax Encounter" The Christmas Invasion, Love & Monsters
30 "Love Don't Roam" (performed by Neil Hannon) The Runaway Bride (except first verse and first chorus)
31 "Doctor Who Theme" (album version) Extended version of the credits music used from The Christmas Invasion onwards.