id Software's Graeme "Zaphod" Devine updated his .plan with an explanation of what that little message of the day number is in Q3Test:

A few of you have asked about the message of the day text. It’s giving you your exe startup number since last Monday. So basically, we’ve had over 2 million Quake 3 Arena games start worldwide since 9/20/99. That works out to around 4 games every second.