Here's a fun little diversion called Upgrade Complete. It's a rather heavy-handed satire of other video-game's overly complex upgrade systems; nonetheless, the game itself has a pretty nifty modular upgrade system that lets you design your own ship. Behold my creation!
Despite being humorous, I found the game's satire a bit superficial. While attempting to criticize overly complex upgrade systems, they managed to create one of the funnest upgrade systems I've ever seen in a flash game. To me, that proves a game CAN be fun solely one the merits of its upgrade system. Pot calling the kettle black much?