"An Accent Beyond", a fast paced tune that fits perfectly with the situation.
How about Bombs for Throwing at You, Wheatley's final boss theme? It's like 'You Can't Escape, You Know', GLaDOS's final boss theme from the original, except it is faster, more frantic, and has some of Wheatley's Leitmotif mixed in at some points.
"Don't Do It". It's played twice, first during the confrontation with GLaDOS, and again at the analogous spot in the Final Boss battle. What's awesome is how it starts out calm, then grows in intensity at "Please press the Stalemate Resolution Button", and then goes freaking nuts after the Booby Trap goes off.
With the release (of the first volume, at the time of writing) of the official soundtrack, we now have The Courtesy Call from the opening without the voice over. And it's as awesome as you imagined it would be.
Caroline Deleted. Even without knowing the context of the song, you can just feel that something bad is going to happen about half-way through... even though something good happens instead.
Your Precious Moon, the music that plays when Chell fires the Moon-portal. And yes, it is appropriately awesome.
Vocal,Semi-Vocal
The ending song, "Want You Gone", (spoilers, of course) is really good too.
There's something about the music box version of the turret opera that just drives you to tears.
And during the game you can find some of these turrets singing this.
"Wheatley's Song", by Miracle of Sound.
PotatOS Lament. This song only plays on the title screen while you're in the old Aperture Science testing spheres, but it's one of the most haunting, etherial melodies in the entire game. Despite the digital effects and the nigh-incomprehensable lyrics, the sheer emotion in GLaDOS' singing is enough to make you want to shed a tear.
"This Is Aperture", a Portal-themed take on "This Is Halloween". Some of the voices in there are so good you'd swear they were the original VAs.
Love As A Construct, a beautiful track to accompany a relationship that will never be until the ending
There She Is, a gorgeous tune that plays as Chell and Wheatley enter GLaDOS's ruined chamber. It's haunting and even somewhat intimidating, and it fits the scene perfectly.
Wheatley Science. It's sinister, mischievous, and almost Danny Elfman-like, and hints at just how badly the Enrichment Center is doing under Wheatley's control.
Machiavellian Bach, actually. Now that volume's out. Adds all the bits together, for better, um, book-reading. One of Machiavelli's best songs, that, I know, not a moron...
Also, the electronic version of the song that plays when you're being flung, and the mixture of the two. If you're wondering, this is where it came from.