The most frustrating modern videogame bosses

[DarthMol]

Really? Were you aware of the mechanics of the yellow crystals against the wall? I only ask because thats the difference between a 2 minute boss fight and a "now i only have the alien gun" moment

Yellow crystals? Nope, defeated him by launching myself up in the air and shooting him on the top of the head with my rocket launcher. I must admit the Xen section was for the least enjoyable of the whole game. So more from impatience I resorted to cheating as I got tired of dying and the teleports.

[mottamort]

Yellow crystals? Nope, defeated him by launching myself up in the air and shooting him on the top of the head with my rocket launcher. I must admit the Xen section was for the least enjoyable of the whole game. So more from impatience I resorted to cheating as I got tired of dying and the teleports.

Fair enough...but that might have been the reason for your frustration (if only with the boss, not the whole environment). Taken from the wiki:
A series of gold-colored "energy spheres" orbit around the Nihilanth's head, rendering it impervious to damage. These are consumed as the Nihilanth takes damage, but specialized crystals within the upper portion of its chamber replenish the spheres as they vanish. After Gordon destroyed these crystals, the shield put up by the orbs will not regenerate anymore. After a massive amount of damage is done, the shield drops and the orbs disappear, leaving his body exposed and susceptible to damage. At this point, the glow of his brain is visible through his head.

After a large amount of damage is done to the Nihilanth's body (more than it takes to blow up an M1A1 Abrams) the Nihilanth's head opens up like a flower, revealing a shining, vulnerable brain. After a significant amount of damage is done to this, the Nihilanth floats up to the roof of its chamber and dies in a massive green explosion.