Note: Blue Shift and Opposing Force's soundtrack was replaced with Half Life's if you bought a Steam copy. Keep this in mind if you plan on making Justifying Edits or corrections.
Black Mesa (Half Life 1, Opposing Force, Blue Shift, Decay)
Half-Life's credits theme and its remix in Half-Life 2. Both tracks are still fairly oddball, but actually have a somewhat jovial mood and, uniquely, human vocals. It's the perfect way to celebrate Gordon's accomplishments and cast a hopeful light on the state of humanity, which offsets the weight of each game's suspenseful and ambiguous endings.
The final boss theme for Opposing Force, Alien Forces, has a lot of stopping power. The alien things have mustered a huge portal underneath Black Mesa, there's a titanic living WMD about to crawl through to our world and it hinges on you to stop it. Now put on your war face and march, Corporal. You have an alien god to punish.
The VALVe theme song, also known as "Hazardous Materials", is especially awesome when the extended version is played when Gordon gets his HEV Suit back in Half-Life 2.
Its first appearance was in a psuedo-boss in Surface Tension, in which you must scale a thin cliffside while facing off against a turret, HECU, and an Apache.
How about some CP Violation? It's not head-rockingly awesome, but it aptly reflects how the CP units (and by extension, the trans-humans in the games) are a fusion of familiar and alien concepts.
Guard Down happens as soon as you kill the Antlion Guard after escaping the Hospital. And then, the music leaves you feeling like you literally let your guard down, and that this moment of calm will only be met with more firefights.
...And even after you're about to leave the condemned Ravenholm, Requiem for Ravenholm will ensure it never leaves you.
Dark Interval from Half-Life 2: Episode Two. The first half makes the Combine Advisors' unexpected attack seem all the more terrifying... and then, halfway through, it punches you in the gut with a haunting, mournful melody that plays over the credits.
Neotokyo, a mod for Half-Life, has some great original songs composed Ed Harrison.
The main theme for Black Mesa. It's very different from the usual electronic music you listen in the games, but it fits perfectly when you think how bleak Gordon's situation during the resonance cascade incident is - he doesn't know if his friends are alive, he has to fight constantly and even against those who were supposed to be the survivors' saviors, and things just get worse no matter what he does. It just pictures him having time to take a break, sit down, and think of everything that has happened, and still is.