we've sent latex balloons up to 120k feet (close to 25 miles straight up!) the main limiting factor is how much does your material stretch? In the case of a typical party balloon, not much. couple thousand feet for a well inflated balloon, higher for a saggy one. Also, helium leaks through basically any material you use it in, which does affect the results, and also temperature drops.

The final limiting factor is where basically the density of helium is equal to the surrounding environment, and that turns out to be around 130-150k feet up, depending quite a bit on location, time of year, sunspot cycle... Hydrogen helps little, but also makes it easier for the hydrogen to leak out of your transport.

Ryan
http://balloons.space.edu