I started playing with Classic D&D (which still used the SIWDCΧ order) and AD&D 2e (where the SDCIWΧ order originated), and I always liked the latter better. It made sense to block the stats into three physical and three mental, and I didn't really understand at the outset where the Classic arrangement had come from (namely, it was ordering the prime requisites of the classes from commonest to least common — the backbone of an adventuring party is supposed to be fighters, followed by magic-users, then clerics, with thieves least important of all, and finally the two stats that weren't core primes). Plus, the rearranged order has been consistent throughout every edition of D&D since 2nd (except 4e/13a) and also the Pathfinders and C&C.
But now that I'm playing an OD&D/AD&D mash-up with a system of nine base classes, I'm arranging the stats in a different order — Str, Wis, Cha, Dex, Int, Con. I'm doing this for largely the same reason that the original game used its order: to help conceptually organize how the character classes fit into an adventuring party. The first three stats — Str, Wis, Cha — are the prime requisites for the commonest character classes, Fighter, Mage, and Cleric. The next three — Dex, Int, Con — are for the more support-oriented classes, the Thief, Artificer, and Monk. And the stats pair off for the remaining three rare classes — Str & Wis for Rangers, Cha & Dex for Minstrels, and Int & Con for Psionicists.