This probably doesn't fit here, since it isn't a Flash game that you can play at work, and it isn't free, but you can definitely waste a ton of time with it.

Universe Sandbox is simply amazing. Makes me wish this was available when I was in school, rather than doing everything by hand. Like I said, isn't free, but there is a timed demo and it is only $9.99 on Steam, so pretty close to free.