Redundancy, Redundancy, Redundancy. This is the magic law in any balloon project. For that reason, you will want to pick out a secondary tracker. You will probably want to pick a tracker that uses a different technology than your primary. For instance, we had a HAM radio as our primary tracker, and a 3G/Cellular GPS for the secondary.
This 3G/Cellular tracker is called the PocketFinder. It's a small Oreo™ shaped object that transmits its position to http://www.pocketfinder.com
You'll want ro order it with 2 months free tracking. This is pretty beneficial. The instructions are pretty simple, but make sure you have it working before you put it in the balloon.
The PocketFinder is pretty accurate as you can see from the image below. This is a screenshot on my iPhone from the actual place where we found the payload in a 60 foot tall tree. The parachute and radar reflector are still stuck there, so if you want to go get it for me, that would be great. Just kidding.