Zero-pressure v. superpressure balloon.
After a post in one of the recent article forums, I've been doing some digging about home build zero pressure or superpressure balloons.
I can understand the reasoning for choosing a weather balloon. They are cheap (relatively anyway), easy to obtain, no fuss in getting them back down, lots of previous knowledge to go by.
But from what I can find, for rockoon flights the big boys (NASA and the likes) seem to be using zero-pressure or Polyethyleen film valved super-pressure envelopes. The advantages of using a zero-pressure design are big. The balloon soars to a maximum altitude and stays there until commanded to drop, thus giving you a much larger launch window and a lot less fuss about how to time the launch. (Just use a timer long enough that you can be sure the balloon reached (near) maximum altitude). There seem to be quite a few HAM radio enthusiast using homebuilt zero-pressure balloons for high-altitude flights.
For instance there is this "tutorial": http://diydrones.com/profiles/blogs/team-prometheus-how-to-make-a-zero-pressure-high-altitude-balloon (look in the comments, the author posted the tutorial amongst the comment thread, not the most readable, but it seems a good guide)
The University of Cambridge seems to have dabbled in high altitude ballooning as well, might be worth it to give them a ring. (http://youtu.be/uK80MXHQ5hA)
A variation is the valved super pressure balloon. This design maintains a slightly higher inside pressure, but limits the pressure differential through a spring loaded valve to just below burst pressure. This has the advantage of a slightly more rigid envelope, keeping its shape better in gusts of wind.