Pandora's Box is from a story in Greek mythology. Pandora was supposedly the first woman made by Zeus. She was given the box as a test of temptation. Predictably, she opened it. Every bad thing came out of it, including fear, hate, illness, anger, and others. But after that terror, one good thing came out: Hope.
The box itself represents human temptation. Like tempting players to use cheats in SRB2.