For a computer science major, you might really consider learning Linux. If you son is serous about Computer science, Ubuntu is NOT a good system because the configuration files are a mess. This might not sound bad but if he wants to really get into the os, it is a nightmare. It can take 30 minutes to sort out a simple file. For someone in his position, it might be fun to install Gentoo to learn about Linux. Gentoo is source based, so most programs are available earlier, the package management is much better than Ubuntu. It takes a lot of time to install, but if he just built the box...
Because it is source based, you get long compile times with minimal time savings running software, but you only get the software you want. This means faster boot up. If you have time to spend on working with the computer to get it to boot up is acceptable, you will get a very nice system AND know Linux. If you install something else, you won't. The handbook can be found here . Read it CAREFULLY and you should be ok, but this is major geek land, so watch you step. You cannot break you computer this way, so at worst you will lose some time.

If you just want something simple, Sabayon is very nice for less work, but is a bit excessive with pre-loaded packages.

      I would recomed looking at the distros in this order:
      
1. Gentoo (if you can spare the time to learn it)
         
2. Sabayon (easy to install, package management a little weird)
         
3. Ubuntu (protected form the user. Not good for people who want to mess with their computer.)
      

Since you are not upgrading, go for the ext4 file system. It is faster that ext3. If you want to try a different distro, be careful! DSL works well, but it is only supposed to be run from the CD drive. Some distros may be poorly supported. Others might be targeted specifically to a group and not support other uses easily. Sabayon is derived from Gentoo so it may be a good alternative if you do not want to try Gentoo directly. The weirdness in package management comes from having a "cute" gui that, well, does not work well on 1G of ram.
THERE IS NOTHING BAD ABOUT LEARNING A COMMAND LINE, ALL LINUX USERS SHOULD KNOW HOW!
As for exactly what permissions and distros are precisely, it does not matter. You can worry about that after you learn the basics. Just remember, as Linus Torvalds said, ""Regression testing"? What's that? If it compiles, it is good; if it boots up, it is perfect."
Happy compiling! uh, I mean installing!