I prefer the newer for a few reasons. Although both the logos represent something about Nemesis (the older representing the monster itself and the newer representing the tonnes of steel used to hold it down), I think the newer logo is far better-looking and more sophisticated - and more scary.
And as has been said above, it fits in more with the rusty, apocolyptic feel of Forbidden Valley.
Also, I associate most of my experiences of Nemesis with that logo. I remember looking at it at the entrance the first time I ever saw Nemesis and at 12 years old being absolutely terrified. That logo brings back a load of great memories, which I never had with the older one.
So yeah, the 'new' one.