Either Alien: Resurrection or Alien 3. I understand that by getting rid of Alien 3, the shitty sequel would be gone, too, but it's a tough call. Alien 3 wasn't great, and it did negatively impact the otherwise perfect first two films. I was, however, pretty entertained by it (and still am, even to this day). And it has Lance Henriksen in it. I have would have trouble deleting any of his career, because he's fucking awesome.
I'll tell you what...if deleting Alien 3 means it will also rid the world of both AvP films (except the scenes with Lance in them), I'll do it. Aside from that, get rid of the Resurrection abomination.