What am I supposed to do when this happens:
In Crysis I always see the culprit: one CPU core at 100%. But in Warhead?
46fps with barely 30% GPU load and every CPU core is below 50%.
That's not fair. Where is the bottleneck?
Crysis is not threaded for more than 2 cores, and even that I believe is with sound/network/small extra things being offloaded on the second core. It is very badly optimized for more than a single core because it is a product of its time, when CPU's were encouraged to be fast single processors for gaming.
Crysis will bottleneck with EVERY processor right now because of how it's designed, no way around it. Want extra FPS? Overclock your proc to 8.0 ghz with some Liquid Nitrogen.
Warhead is better threaded, and that's why you don't see 100% usage on one core at all times, so your FPS is probably being limited by some other component, most likely memory bandwidth or GPU processing power. Don't go by GPU load exactly, increase GPU memory and Core clock rates and see if your FPS goes up proportionally.
System specs would be helpful as well
P.S. - Pretty much every game now is being designed to take advantage of multiple cores, Battlefield 3's complexity is a great example. I get activity across all 6 cores and smooth 60 fps, the same game on my Dual Core was constant stuttering with both cores at 100% (MOBO, RAM, AND GPU identical in both tests).
Basically, you won't have this problem in the future. Multiple cores are the way to go now with gaming, you just happen to be playing two games that were on the bleeding edge of technology at the cusp of when the transition to multiple cores for gaming started to be recommended.