Directory order won\'t really matter much. The files will all be reorganized when you do your optimizations, and since you generally don\'t run say, two games at once, it won\'t matter if they are next to each other physically, or not. If you want them to perform at their best, when you optimize, specify for the game files to be at the end of the disk, so that they\'re on the outside of the disk, hopefully going fastest.
Really though, you aren\'t going to get as much of an improvement by doing this as you will by checking your background processes and such.