My 2 cents on the Mac Mini:  Don't force them to "switch" unless they both tell you they'll be OK with that.  Also, consider the cost of MS Office for OSX down the road, which will be necessary for the first one that hits college.  (Also, an external floppy may be necessary for moving papers, etc., between school and home, depending upon the remote access/storage capabilities of the college network.)
If building a PC, I think integrated graphics would be fine, as would a different Antec case, such as the SLK1650xxx or SLK3700xxx.  (You're on the right track thinking of Antec cases in order to get a good PSU, but there's no need for more than 350 watts when you're not going to be running an Intel Prescott P4, nVidia 6600/6800, or overclocking.)
I'd also drop down to a 3000+ (if building my own, I'd get a Winchester because it runs cooler, saving energy and allowing for lower fan speeds) and spend a little extra money on a brand new hard drive unless the one you have is almost brand new--today's drives don't seem as long-lived as they used to.  I prefer Seagate these days; I've had 4 of them (model# ST3120026A) running almost 2 years now, 2 in the PC, 2 in the Tivo, with no problems at all.  (knock, knock)