Well. It depends.
How much experiance do you have with Linux so far? It's quite a bit different from Windows and can be a challenge to new users sometimes.
Linux is open source. This means that any person has equal access to the source as any other person, so what happens is the distros (different versions) generally have the best they can get and utlimate performance is about the same either way.
It also means that you can obtain most versions for free from the internet. linuxiso has links to many different downloads,
http://www.linuxiso.org/
Some distros have only x86 aviable (32bit versions) others have both 32bit and 64bit aviable (called x86-64 or AMD64, something like that)
Some distros that have mature 64bit support are Mandrake Linux, Gentoo, Suse, and Redhat. Out of those Mandrake, Suse, and Redhat will probably be the most usefull for you.
Redhat sells several different versions of their OS and it can only be obtained by buying it. When you buy it you enter into a support contract for a year of updates and 30 days of configuration and installation assistance. (depending on your purchase you can increase support for up to a year) The desktop version is Redhat WS. You can find this stuff out and were to buy at
www.redhat.com
Redhat may be worth looking at if your Dad wants to use commercial tools on it. It is the most common distro and is certified to run a large number of closed source and commercial applications on it. Some applications will only run on Redhat.
If you don't want to pay for it there are free clones of it like Whitebox or CentOS that are pretty much the same thing.
However it's not quite the most up to date version you can get.
Another popular version that has certification is Suse. Suse is one of the first distros to support AMD64 natively and is less expensive (and much more up to date) then Redhat. However less commercial closed source software has certifications for it.
Currently there are several ways to obtain Suse. Suse has a few different retail versions. The one your probably interested in is Suse Professional 9.2 and it comes in a box set with some manuals and installation sets for x86 (they call it IA32) and AMD64. That sells for around 90 dollars.
For free versions you have:
http://www.novell.com/products.../suse_linux/index.html
You can download the FTP install version. This is were you download a small ISO image for a cdrom and you boot up on a computer. Then you set it up so that as your installing it downloads the software from a online FTP site. This is the best way, but it can be difficult for a new user.
You can download a live-eval version. This is a DVD ISO image you burn to a DVD (as a ISO image, instead of copying it over). This boots up and runs completely off of the dvdrom without installing anything on your harddrive. It is provided as a way to try it out with no risk to any information on your harddrive.
You can download a DVD install ISO image for Suse 9.2 professional. This has everything you need for both the x86 and x86-64 versions. (I beleive. I haven't tried it out, but it should be that way).
Mandrake is suppose to be very user friendly, but it's also the least likely to have commercial support for many closed-source applications. It has a fairly inexpensive retail version and a free version that is aviable for downloading that is released quite a bit after the retail version is released.
http://www.mandrakelinux.com/en-us/
I am thinking that your best bet is for one of the free versions of Suse you can download. Either the FTP version or the Eval version.
If you want the extra manual and the support that Novell/Suse provides then buy the retail version. But I wouldn't do that unless you knew that the software that your dad wanted to run would work well in it.
Your hardware choice is OK, but I'd stay away from Nforce-based motherboards because of their propriatory drivers. Via motherboards can be nice, but if you have your heart set on a specific nvidia board, then that's OK. It will work fine. You may run into issues if the Nic card doesn't work and you need to download the drivers to get it to work though.
Also you would have to download propriatory drivers if you want accelerated 3d performance from your card. (also shop around for those cards, you can probably find a much faster one for not much more expensive.)
here is some advice on buying computers for a Unix workstation. He suggests a nice ASUS motherboard and ECC memory. The ECC memory may be a to big of a bump in price, though. It's up to you. He recommends a older ATI card. These older cards have support from Linux automaticly because there are open source drivers aviable. (for versions up to 9200). Anything newer you have to use propriatory ATI drivers.. Which SUCK. Nvidia support for newer cards is much nicer.
Memory is the one thing that I've had trouble with on building these AMD64 machines. They have the memory controller built in the CPU and I think this makes them touchy, so be sure to make sure that what brand and type of memory your getting is on the list of recommended types of whatever motherboard you choose to get.
Good luck and check out the link in my sig for some guides if your not familar with Linux. They are more designed for administrator type, but I think that they could be usefull for most people.