Boson X is sciencey, also Free

Boson X is a simple time-waster gamey-thing, which has been making quite a furor in the indie game world. Turns out it's not only available gratis, but it's also Free Software. It's quite a challenging little game, but oh, if only particle physics were this easy. So if you want to experience all of the thrill of being on the edge of a scientific breakthrough with none of the insane amounts of reading and complex calculations (and actual breakthroughs), give it a try.

I wish actual science was more like this

The source for the engine is available here under the MIT license. The game itself is completely scripted in lua, so will find all of the required data inside the game package itself. Spread it, port it, package it, but remember all of the artwork as well as the brand name are copyrighted.