Which version is better? Are the extras the same minus the seperate music CD in the Delux edition. I've seen the SE at Wal*Mart for 7.50, is the Delux edition that much better?

I think the deluxe edition (brown cover) is the same as the special edition, except that the deluxe edition had a extra CD (the soundtrack).

Deluxe:
http://www.dvdtalk.com/reviews/read.php?ID=7889

Special Edition: (1 Disc)
http://www.dvdtalk.com/reviews/read.php?ID=1106

They are identical except for the packaging and the score. If you have the dough, though, go for the Deluxe. The score for Rudy is absolutely fantastic, a must own CD.