Back in high school football, it was all about endurance. We did something called indian run, where the entire team would run a fast-paced jog around the field for a set interval of time (usually about 25-30 minutes). Every minute or so, the coach blows the whistle and a player sprints from the very back of the line to the very front. I was in shape (about 250 lbs. at the time, which is in shape compared to my weight now), and I could usually keep pace for about 15 minutes or so before I started breathing really heavy. By the end you're grateful you made it out alive, let alone whether or not you kept pace.
Also someone mentioned gassers which can suck a whole back of cocks. They were usually only a once-a-week exercise, but whenever we did them we'd usually run a fuckton and it would be terrible.
Heh, and those were just for conditioning, not even getting into punishment runs. One time a few of our players were fucking around during stretches, and our coaches made them sit in the middle of the field while the rest ran suicides for the entire length of the football field. Bull in the ring was popular as well, where one player gets thrown in the middle and has to hit the shit out of someone in the ring paced to the coach's whistle (basically one hit ~5 seconds for about three minutes, then the next player goes).
The worst I ever saw was when someone got caught drunk in class and had to run up the river down the river. For the uninformed, this is running the width of the lines on the football field that mark every five yards on the field. Up and down, all the way across the field, and all the way back.
The beep test doesn't look that hard, looks a fucking ton easier than 40's or gassers.