There are numerous reasons why, and I'm doing a Top 5 for this.

Top 5 Reasons why Naruto characters run with their arms behind their backs:
1. It's cheaper! (Cash is king people. Don't underestimate the miserly cheapos' determination to cut costs)

2. Master Shikamaru's point. Arms back can be used to deliver a more powerful first strike or throw. It is also harder to predict the angle of attack from that arm position. On the con side, because the arm is so far back, the strike is slower (simply a larger distance to cover), giving the enemy opportunity to block/parry.

3. Aerodynamics. They are running really fast already, i guess they don't need the extra momentum (or balance) provided by swinging the arms back and forth. Although... for guys like Chouji and other "bungler" types I would imagine they'd be a little slow/unbalanced and would need to swing their arms... Also, maybe the high speed does cause the arms to get pushed back. I'm no physicist (sp?)...

4. Its just one of those anime traditions. Why does raising energy levels cause the ground to float upwards and defy gravity? How can enemy mobile suit pilots talk to each other amidst a raging battle, through sheets of metal, in the void of space, when no military would ever share a frequency with their foe? How does their hair stay so perfect all the time? How come the guys look so girly? How come a main character at some point in a series 'dies' only to return to the battlefield episodes later? Why do they draw the girls' boobs so disproportionatly bigger than their tiny waists could ever suppport? Why the fuck isn't Kira Yamato dead? Answer: Anime tradition.

5. God made ninjas retarded. He gave them super speed, stealth, precision and endurance, but He forbids them from using their arms whilst running. Amen.