For the intense multi-threaded ray-tracing C-Ray test and the computationally intense Crafty, there were no differences between the kFreeBSD and Linux variants.
7-Zip compression was 19% faster with the Linux 3.2 kernel over FreeBSD 9.0.
Debian GNU/Linux with the EXT4 file-system was many times faster than Debian GNU/kFreeBSD with its default UFS file-system.
The MAFFT molecular biology test was multiple times faster on Linux than kFreeBSD.
While MAFFT was faster on Linux, Debian GNU/kFreeBSD finally scored a striking win when it came to the MrBayes molecular biology benchmark.