Like I said, I don’t know what the pilots take or don’t take. I’ve not heard much about Navy pilots taking them, but I work mostly with helo pilots who don’t fly missions that are generally 10 hours long. The don’t give any of that crap to us ship drivers. Nothing but Mountain Dew and Coffee for us, and we like it that way. 
In Air Force lingo, these are “go pills.” There are two types. Dextroamphetamine, or Dexedrine, has been around for decades. In November 2003, the Air Force approved Modafinil for use by bomber, tanker and airlift pilots. Lieutenant Smith helped test the new drug on F-117 Nighthawk pilots. It was something she said was important and exciting, because unlike Dexedrine which has side effects, the new compound is different.
“Nine out of 10 of the pilots couldn’t tell they were even taking a drug,” she said. “But it was still helping their performance.”
http://www.af.mil/news/airman/1204/nerd.shtml
And looks like there’s some use, if less, inthe Navy too
Still, extended flight missions have been routine for decades in the armed forces — usually without the benefit of the pills. Navy aviators, for example, only began using Dexedrine in November of last year, well into the Afghan campaign. (Navy doctors approved a go-pill program in 2000.)
“Our standard mission was 10-12 hours and there was never any suggestion that we take anything,” says retired Navy Capt. Charles “Chuck” Sipe, who flew Cold War patrol missions in a P-3 Orion and now teaches at the Naval War College. “If you’re too tired to fly, you don’t take a pill to boost your endurance. It’s a bad idea.”
http://www.msnbc.msn.com/id/3071789/
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On a related note, a lot of medical students/residents rely on caffeine pretty heavily though some intense rotations where it’s hard to get much sleep… I wonder what the prevalence of other stimulants is?