Of course, there really have been projects that used balloons in the upper atmosphere. It is actually difficult to maintain a balloon at a constant altitude in the upper atmosphere because you have to account for daily temperature variation and changing wind patterns. The most famous project of this sort was Project Mogul[4], which attempted to put a balloon in the atmosphere's analogue of the SOFAR channel to listen for anything that sounded like a nuclear test in the Soviet Union. One of the Project Mogul balloons crash landed in Roswell, New Mexico in 1947. The government's cover story was that it was a "weather balloon", which of course, it wasn't. But it wasn't an alien spaceship, either.
[1]: http://thedailywtf.com/Articles/Virtudyne_0x3a__The_Digital_...
[2]: http://www.hp.com/hpinfo/newsroom/press/2004/040707b.html