Actually, most stuff by Chameleon Circuit deserves an honourable mention on this page. It might not be actually heard on the show, but it's all one great big celebration of everything which makes the show awesome.
Classic Doctor Who (1963-1989; 1996)
The epic guitar riff from Survival that plays on the cheetah planet.
Paddy Kingsland's music for Logopolis and Castrovalva was beyond cool.
Although it was really just a simple bit of 80s incidental music, the haunting "flashback" music that plays as the Fourth Doctor is seeing the images of his old enemies taunt him before he falls is unforgettable.
...And the slow descent of single synthesiser tones down a minor scale as we see him lying on the floor just prior to regeneration. Very simple and yet very effective.
The background music during the Daleks' fight with the Mechanoids at the end of The Chase is also pretty awesome.
The music in Androids of Tara, especially that absolutely gloomy wedding march in Part 4.
The fabulous, Gershwin-inspired "running through Paris" music from City of Death.
Everyone seems to hate the "Sea Devils" soundtrack, calling it a glorified series of electronic fart noises- listen to this arrangement, which captures the most eerie parts of the music and avoids the least well-regarded snippets.
The soundtrack for The Invasion, a cross between a soundtrack from a western with one from a spy thriller.
The soundtrack from Remembrance of the Daleks is '80s-licious, especially the bit (0:00 - 1:15) where Seven and Ace are tearing down the street with the Daleks hot on their heels.
All of the music from Mawdryn Undead was fantastic, making it even more amazing than it already was.
The opening music from the first episode of "Trial of a Time Lord", with the epic computer-controlled whirling shots of the Time Lord space station, all done with model effects that, in a rare moment for classic Doctor Who, still hold up as excellent today-watch it here. Definitely the best bit of "Trial of a Time Lord" and the most expensive special effects done on the original series (it shows).
The Ambassadors of Death has a catchy synthesizer tune which shows up a few times and can be heard in its entirety in episode 2, when the UNIT convoy drives Recovery 7 back to the space center.
Planet of Fire had an atmospheric soundtrack for many of the scenes set on Sarn.
That song was used in the final few minutes of "Turn Left". As the Doctor questions Donna on the alternate reality that had been built around her, the music is soft and in the background. Then when she talks about Rose, the music picks up, and when Donna passes on the message, "Bad wolf", the music picks right the hell up and punches you in the gut. It's fast and crazy and can't help but get your heart pounding.
The scene in question, you can clearly see how the music builds up with the Doctor's Oh Crap face.
Also used to great effect in The End of Time as the Doctor finishes his frantic race back to Earth to face The Master and Rassilon.
"Doomsday", from the episode of the same name, contributes just as much to the Tear Jerker ending as the acting.
Hell, any music in "The Stolen Earth" gets CMOA syndrome. "The Doctor's Theme" and "Doomsday" get upgrades (the former having first been unleashed in "Forest of the Dead"), whereas "Rose's Theme" and "Harriet Jones, Prime Minister" become awesome without change.
Then there's another not-on-the-soundtracks violin piece you can hear at the end of "The Runaway Bride".
Murray often uses big, bold fanfares in place of traditional tear-jerking cues for emotional scenes, which give them all the more power. The afore-mentioned "Doomsday", the Master's death in "Last of the Time Lords", and Donna's decision to go to her death in "Turn Left". The latter is reprised with Donna's final sacrifice in "Journey's End"; and it's even been bolstered with the riff from "Doomsday".
A slower, sadder version pops up in "The Doctor's Daughter", when, to steal from Russell, "things get Time Lordy".
Behold this bassoon-eriffic, subdued version from the 2010 Proms—followed by the magisterial Vale Decem no less, and showing footage of all the Doctor's regenerations. Extra points for the audience's standing ovations at Pertwee, Tom Baker and Tennant.
Starting Vale Decem 2 seconds before This Is Gallifrey, and playing with the latter's volume just a bit at times, produces a heartrendingly beautiful song. They play off of each other really well... the beginning is a little discordant, but it soon resolves. For example: the swell in T.I.G. at ~1:45 - it's perfectly mirrored in Vale Decem, and that's only the most prominent matchup.
In "Journey's End," when the TARDIS is towing the Earth back home, there is some truly, truly awe-inspiring music: the Oodsong writ large and glorious as the "Song of Freedom". Ten minutes later, however, and it's back to being a Tear Jerker. Thank god Murray isn't leaving the show anytime soon.
The 2008 and 2010 Doctor Who Proms were a glorious Crowning Moment for the series' most bombastic themes, reworked to even more awesome levels.
Props goes to the medley of Martha and the Master's theme as well as "Martha's Quest", aka "Martha vs. The Master".
How awesome did Donna Noble turn out to be? This track sums it up nicely. Seriously, it sounds like the sort of music that would be playing if the girls from Sex and the City were out saving the freaking universe.
Also in that episode, "The Source", which is another one of Murray's gentler and still-epic pieces.
Davros gets his own motif in Series 4, which doesn't quite suit him but is creepy as hell.
That descending brass sound midway through sounded like something straight out of Lost.
And speaking of creepy, just listen to the Blink suite or the music from Midnight. Anyone who can listen to those without looking around in paranoia and getting goosebumps wasn't really listening.
The "Voyage of the Damned" suite from the Series Four soundtrack. In particular, three passages: Astrid's Theme followed by a Braveheart-flavoured rendition of "The Doctor Forever"; the reworking of "All the Strange, Strange Creatures" as the Titanic falls before rising into a glorious instrumental of "The Stowaway"; and the finale with the Doctor's goodbyes to Astrid and Mr. Copper.
"Turn Left" got one of the most chilling themes ever, combining all sorts of recognizable snippets into one haunting piece that NEVER gets old. EVER.
"The Lone Dalek" Not only was it beautifully used during the episode "Dalek" but it was AMAZINGLY used at the end of "Doomsday" (admittedly, most people assume that the last piece of music in that episode is Doomsday or Rose's Theme). But when the music reaches its final climax JUST as the tear falls down the Doctor's cheek as he finds himself alone in the TARDIS at the end...it also has the benefit of providing another point of comparison for the Doctor and the Daleks that a song about a Dalek's loneliness can be used so effectively for the Doctor. This piece of music is one of the most beautiful and haunting pieces of music EVER.
In The End of Time part two, whatever that music was that started up when the Master told the Doctor to get out of the way. That was pure badass. And it's a heroic sounding theme, used for the Master, without feeling the slightest bit out of place.
The song is called Vale Decem, or "Farewell Ten". It's in Latin, and it is actually a true goodbye to the Tenth Doctor. Apparently this translation is a bit rough and inaccurate, but it's close enough for us to get the overall meaning. That made the scene even more meaningful. If it was a Tear Jerker before, it's even more now.
"We will sing to you, Doctor. The universe will sing you to your sleep."
The rousing choral crescendo that plays as the 10th Doctor begins to regenerate in the TARDIS. It's a reprise of "the Doctor's theme" that's been with us since day one of the new series, but it manages to be bombastically triumphant and desperately sad at the same time.
What makes it even more awesome, is that even though the song is sung in a different language, you can hear the singers say the phrase, "God save the TARDIS".
In The Waters of Mars, a fast-paced, action-oriented piece of music begins to play in the climactic scene of the episode, continuing on until the base explodes at the end. It's such a fitting piece that pretty much defines the urgency and heroic nature of the situation, but what's even weirder is that a good deal of the same piece is later used in The End of Time as the Master's plan to turn everyone into himself comes to fruition. It doesn't sound a bit out of place in the new context and now sounds utterly diabolical.
The Eleventh Doctor's theme — "I Am the Doctor" (Version from the 2010 Proms included, for extra goodness). It sounds like the orchestra managed to purify badass down to its essence, drenched their instruments in it, and just started to rock the hell out. You know things are about to get intense.
It's also played over particularly dramatic moments and trailers (like this one), thumping you upside the head to say "This is goddamn epic!"
"The Life andDeathof Amy Pond" sounds like something out of Lost, right down to its name. Beautiful. It plays at the end of "The Pandorica Opens", followed by this eerie reverb of the track that creepily...stops.
All of the Ood song, from the achingly sad "Song of Captivity" to the glorious, uplifting "Song of Freedom". Have a listen.
"The Shakespeare Code" has the track "The Carrionites Swarm", which rivals even All the Strange Strange Creatures in soaring epicness.
The Cyberman theme from series 2 turns into a dark march for "The Next Doctor", ending with a rousing hint of "The Doctor Forever".
"Hologram" alternates between emotional and triumphant.
"A River of Tears" is not only a very haunting piece, it also features backmasked sections, which symbolise River's relationship with the Doctor, always meeting in reverse order. And if you play it backwards you get a similar piece that sounds a little darker and more intense...
The Impossible Planet. Some rather scary, mournful strings, evoking the ancient and impossible setting of the episode of the same name well, before turning to a more emotional piece of Murray's midway through.
"Come Along Pond", which later became used as the trailer music to "The Doctor, the Widow and the Wardrobe".
"Day of the Moon", truly heroic music played in The Girl Who Waited during the scene where Amy, Rory and Samurai!Amy fight off the handbots while heading back to the TARDIS.
Brigadier Lethbridge-Stewart is an amazing piece starting out small and sad, yet quite beautiful as the Doctor finds out about one of his oldest and best friends' death, then builds up to an awesome arrangement of I Am The Doctor that captures the bittersweetness of revisiting the events of The Impossible Astronaut and the death of the Doctor from the Doctor's perspective.
"The Majestic Tale (Of A Madman In A Box)", the epic, triumphant variation of I Am The Doctor that plays as the Doctor defeats the Silence and River's ensuing ass kicking of said Silence in "Day of the Moon".
"Captain Jack's Theme". Pure. Win. Even better, it crops up in the aforementioned "Owen Fights Death". The companions' themes in the Who series tend to be softer, more melodic tunes, but Jack's is exactly the opposite.
Jack's theme becomes even more awesome when you learn that it was written for the end of Countrycide, and is structured around repeated use of the phrase, 'Here he comes in a bloody great tractor.' Which is just kind of hilariously brilliant.
It becomes even more awesome when you realise that as Jack has become more like the Doctor, at 1:08, it's segued into "The Doctor's Theme" and then at 2:00 the melody seems to be a riff on "This is Gallifrey".
"Torchwood Theme" from the credits is pretty cool too. The use of the pattern from "Army of Ghosts" is a pretty neat touch. Also in the first album, "The Chase" is an action theme that makes you want to break into a run.