Near I can tell, it's an oversize human baby with a satellite jammed up its bottom.
What it was doing in the game as the final boss is any non-Valve-employee's guess.

The Typing of the Dead
Perimeter
Sacrifice
Hellsinker
Super Mario Bros.

For modern PC gaming I would go for Anachronox - sucking on a sweaty sock anybody? And Grandad's chatter?!
But for all time gaming it has to be Agent USA on my ol' Commodore 64!!! (Can you get the Fuzzbomb>!)
http://www.filmjunk.com/2000/06/29/agent-usa-commodore-64/

Ah, you mean 'Nihilanth'. It's a larger version of those large-headed, floating, fireball-throwing Mekon wannabe's that attack you in the teleport chamber and bedevil you constantly throughout 'Xen'.
Interestingly (at least, to me...) they're the only non-animalistic alien creatures that are not actually mind-controlled into attacking you. So to me it sort of made sense that a larger version of them would be the Big Bad.
Just my take on it.

I remember a mod for the original UT that I used to play a lot with friends.
It was called Flack rabbits, or something to that effect. Essentially all it did was change the alternate fire on the flack cannon to fire a rabbit, who would land, and hop around quite casually. If you were to go near the rabbit however, it would explode.
I would really like to know what the writer of that mod was on, and where he got it!

Wasn't the point that the Nihilanth was being controlled by the Combine so they could attack Earth with the creatures of Xen?

Weird games -
Mabye Infernal
Lada Racing Club
Fight Club

Sort of hinted at in the sequel, yeah. I was just going off my impressions from the first game, though.

Win.
And it is so beautiful at the same time. I really enjoyed watching it, probably way more than playing the game but who cares.

One I was just reminded of the other day;
Anyone remember the last boss from 'NARC'?
That was seriously messed up...