which of this hard disks is better and why?

WD6400AAKS is better.

This review is about 320GB HDD, but should be applicable to the 500GB ones. Also other information on the site about HDD that should be useful
http://www.hardwaresecrets.com/article/603

Nice review. The info about the WD3200AAKS applies to the WD6400AAKS (same disk, with two 320GB platters instead of one). It applies less to the WD5000AAKS, which doesn't use perpendicular magnetic recording and uses some older technology. The perpendicular magnetic recording makes a huge difference, in my experience. I've got a mix of WD5000AAKS (no PMR) and WD7500AAKS (with PMR) and I can see the speed difference easily. There are programs that stop for two minutes to flush the cache with the WD5000AAKS but don't need to do it with the WD7500AAKS. The WD6400AAKS is even better than the WD7500AAKS.

I think the "ABYS" versions are enterprise-class disks, not really meant for home users. In general the main difference is that they cost more and are supposed to last longer even when used 24/7.

Agreed. +1 for 640 GB from Western Digital (2 platters of 320 GB).