The X11 and 3D performance comparison is not meaningful, as they compare different versions of the NVidia proprietary driver. But other benchmarks are quite interesting.
Originally Posted by http://www.linux-mag.com/id/7574/3/
Although we are not comparing apples to apples, Gentoo did out-perform Ubuntu in almost every test, and sometimes by a fair margin. It does appear that optimizing for a specific CPU can yield a decent performance increase.
Of course the decision for or against Gentoo is not primarily due to performance, as the commenters point out.
@krazy: Phoronix already tested the performance of different kernels. Some tasks are faster and some slower, but the assumption that kernel version skewed the results is not consistent with the almost sweeping win of the 2.6.30 based system over 2.6.28.
Different X server and NVidia driver affect X11 and 3D performance (that is why I said that this part of the comparison is meaningless), but not media encoding, database or similar tasks.
Both systems had the same gcc version and the same filesystem, so I would guess that the compute and I/O results are mostly valid.