The VG Resource

I was thinking of ripping models from the prototype version of Half Life in my free time.

Since it uses different models than the final game, nor does it share anything with the final game. Would this be counted as a different game? Or would I put the models under the Half Life section?

Whatever you do, make sure you specify which unfinished version of Half-Like you are refering to. There is more than one:
September 1997 Prototype
Half-Life: Day One
Half-Life: Uplink
Build 738

Sep 1997.

I already have some models working. Crowbar apparently has issues with some due to dated formats.