Yeah, I would say the Ichthyosaur only causes some anxiety because he swims a LOT better than you can, and has claws. Likewise, headcrabs cause some good “Jump back from the monitor” moments, but not true fear. Doom 3 did it pretty well, where you have the fear of the unknown - noises and shadows, then BAM! Imp in your face.
As far as the Half Life series goes, I think HL2 and the episodes did a pretty decent job in certain areas. Ravenholm definitely gave you a sense of desolation, and a bit of fear due to darkness/fast zombies. But the episodes (I can’t remember which episode had which sequence) had some good scenarios where you’re in a dark parking garage full of zombies with only flares and exploding barrels lighting the scene periodically.
As for BM: S / HL1, I remember Xen used to scare me a little bit - big factory with odd noises, Garg, walking testicle, etc. The assassins caused some anxiety due to their agility. Otherwise I can’t think of much in the game that actually caused “fear”. Lightbulb - the introduction to A.Grunts in (Questionable Ethics?) where you’re weaponless and it busts out of the viewing chamber - that inspired some fear (the first and second time it happened).
Short of that, I think the realism of the models (especially the A.Grunt and Controllers) will help with the fear effect. Guess that remains to be seen 