Well, I'm pretty sure that new Painkiller game uses the Quake III engine. It looks like it, smells like it, plays like it...and he has the same grunt as sarge. hehe. That game is a physics fragfest if I ever saw one. Ragdolls would be pointless in half-life I think; bodies fade quickly and it'd probably make it suffer performance wise, no?
I know Quake III doesn't have rag doll, but as I said above, I've seen games that I'm like 80% certain are using the Q3 engine.
As for the other stuff, well I know it isn't that easy to implement. And thinking back on my original commentary...an engine with all these optimizations would probably be the half-life 2 engine anyway, so I guess I was beating a dead horse.
As for how impressive half-life is/was, I have to admit that I didn't play it until well after it came out (not several years, but maybe beginning of 2001ish). So my opinion is horribly marred and skewed, hehe.