They used Apache 1.3.23 with RH AD, and Apache 2.0.40 with RH 8.

Despite the fact it's a load, Apache 2 is supposed to be quite a bit faster. They only use RH 8 on the dual processor machine (I think). Maybe TUX doesn't work with apache 2.
They're also using kernel 2.4.9-e.3enterprise when testing 2, 4, and 8 processor machines. 2.4.9-e.3 with the uniprocessor machine.
Is 64k bytes the default block size for NTFS on a volume of 60GB (if that matters)?
p33 mentions the encryption stuff.
Operating system: Key exchange algorithm, encryption, message digest
Win2k3: RSA, RC4 (128-bit), MD5
RH AS 2.1: diffie-helman, 3des (168-bit), sha1
RH 8: diffie-helman, 3des (168-bit), sha1
rc4 is not only faster than 3des, it's absolute shit.

I'm not sure how RSA compares to DH, but they're both good systems.