I'm very happy the headphone jack will be at the bottom. When I put my phone in my pocket, I put it in head first so when I pull it out, it will be ready to use. That little flipping motion, plus having a cable jabbing out (especially on the train) gets in the way. The bottom is the best way to have it in a city. If I were just in the town or in the country, I may not care so much, but Tokyo necessitates clean, tight designs. Strange that Japanese companies don't think of that and make big, ugly, and overcomplicated stuff.
Cant say I like the look of this pre-release photo - unlike the image above, it has the headphone jack at the bottom of the iPhone :
Commonsense dictates that you wont be listening via the headphone-out with your LOD/CLAS etc connected, but I don't see what the problem was with having the headphone out at the top of the phone. Much easier to listen with the thing on Shuffle in a pocket/satchel etc. Presumably Apple will make the same changes to the next generation of the Touch - no idea what they will do with the other models but ditching the 30-pin connector is reportedly due to the number of obsolete pins in the old connector.