Ah, Doctor Who... and Muse. I fell in love with these two around the same time and that's why they kind of, sort of always belonged together for me. Confidential helped with that too, because the Confidential people liked to use Muse songs. And to find out how much exactly, I started a list. It was supposed to be an ongoing list, but, you know, Confidential got cancelled. :o(

season 2 | season 3 | season 4 | specials | season 5 | season 6

Doctor Who Confidential	Muse song
1x01 Bringing Back the Doctor	/
1x02 The Good, the Bad and the Ugly	/
1x03 TARDIS Tales	/
1x04 I Get a Side-Kick Out of You	/
1x05 Why on Earth?	/
1x06 Dalek	/
1x07 The Dark Side	/
1x08 Time Trouble	/
1x09 Special Effects	/
1x10 Weird Science	/
1x11 Unsung Heroes and Violent Death	/
1x12 The World of Who	/
1x13 The Last Battle	/

2x00 One Year On	/
2x01 New New Doctor	Feeling Good
2x02 Fear Factor	/
2x03 Friends Reunited	/
2x04 Script to Screen	/
2x05 Cybermen	/
2x06 From Zero to Hero	/
2x07 The Writer's Tale	/
2x08 You've Got the Look	/
2x09 Myths and Legends	/
2x10 The New World of Who	/
2x11 The Fright Stuff	/
2x12 Welcome to Torchwood	/
2x13 Finale	Hysteria

3x00 Music and Monsters	/
3x01 Meet Martha Jones	/
3x02 Stage Fright	/
3x03 Are We There Yet?	/
3x04 A New York Story	/
3x05 Making Manhattan	/
3x06 Monsters Inc.	/
3x07 Space Craft	Time Is Running Out
3x08 Alter Ego	Knights of Cydonia
3x09 Bad Blood	Take a Bow
3x10 Do You Remember the First Time?	Starlight
3x11 'Ello, 'ello, 'ello	Supermassive Black Hole (DT says 'lost the plot' about the Master)
3x12 The Saxon Mystery	/
3x13 The Valiant Quest	Invincible

4x00 Kylie Meets the Doctor	/
4x01 A Noble Return	/
4x02 The Italian Job	/
4x03 Oods and Ends	/
4x04 Send in the Clones	/
4x05 Sontar-Ha!	/
4x06 Sins of the Fathers	/
4x07 Nemesis	/
4x08 Shadow Play	/
4x09 River Runs Deep	/
4x10 Look Who's Talking	/
4x11 Here Come the Girls	New Born
4x12 Friends and Foe	/
4x13 End of an Era	Map of the Problematique
4x14	/

The Eleventh Doctor	/
4x15 Desert Storm	/
Greatest Moments: The Doctor	/
Greatest Moments: The Companions	/
Greatest Moments: The Enemies	/
4x16 Is There Life on Mars?	Radiohead, LOL.
4x17 Lords and Masters	Uprising
4x18 Allons-y!	/

5x01 Call Me the Doctor	/
5x02 All About the Girl	/
5x03 War Games	/
5x04 Eyes Wide Open	Uprising
5x05 Blinded by the Light	Resistance
5x06 Death in Venice	/
5x07 Arthurian Legend	/
5x08 After Effects	/
5x09 What Goes on Tour	/
5x10 A Brush with Genius	/
5x11 Extra Time	/
5x12 Alien Abduction	Exogenesis: Symphony Part 3 (Redemption)
5x13 Out of Time	/

6x00	"Aiming for it to sound a bit like Muse" says Murray Gold. :oD
6x01 Coming to America	/
6x02 Breaking the Silence	/
6x03 Ship Ahoy!	/
6x04 Bigger on the Inside	/
6x05 Double Trouble	No Muse in this Confidential, but Supermassive Black Hole was played in the Doctor Who ep! :oD
6x06 Take Two	/
6x07 The Born Identity	/
6x08 River Runs Wild	/
6x09 About a Boy	/
6x10 What Dreams May Come	/
6x11 Heartbreak Hotel	/
6x12 Open All Hours	/
6x13 When Time Froze	/