There are a number of groups that have used cell phones to track their balloons, but it doesn't come without its challenges.
First of all, it may be illegal at least within the United States. The FCC has forbidden cell phone usage on board aircraft, and a unmanned free balloon qualifies as an aircraft as far as the FAA and FCC are concerned.
More importantly though, there are some severe limitations to the cell phone technology that don't lend themselves well tracking high altitude balloons. Most GPS's in the market today are incapable of tracking position when the altitude exceeds about 60,000' above sea level. This has to do with an obscure regulation regarding the usage of GPS technology on board ballistic missiles, but GPS manufacturers will often kill the tracking above this altitude to remain in compliance. There may be exceptions, but you can assume that most cell phone manufacturers safely assume that their users are not going to be traveling into the Tropopause and won't need this feature.
Next, cell phone reception can be pretty spotty when you're 20 miles (above) the nearest cell phone tower, as well as when the phone is sitting on the ground, potentially miles from the nearest service road. Hence, the last position report you may get could be from thousands of feet in the air, and the balloon could have traveled quite some distance from that point, to where it is actually laying on the ground.
The last point about cell phones is that they don't tend to be hardened, application-specific devices that have a lot of redundancy built in. They tend to crash, reboot themselves, or behave in other unpredictable ways that may interrupt your tracking abilities, some of which would be impossible to test until you release the balloon.