The best way of thinking about the game is a Puzzle Quest-ian take on the TD genre. You're trying to protect your base from oncoming hordes with varying strengths and weaknesses, but instead of building different types of towers, you use mana to create different gems that are placed in towers. Each color has different qualities and if you're willing to spend more mana you can create stronger versions of each, creating a risk/reward question of building a weaker gem or waiting to build a more powerful one.
There's another layer on top of that, though. As you complete stages, you earn experience that you can use to buy more starting gems, a lower mana cost for gems, quicker mana regeneration, etc. And each time you beat a level with more experience, the difference is added to your total. That means that while it may be easy for you to beat the opening stages, if you don't work to get the best score you may not be powerful enough for some of the final conflicts.
There's a lot going on here, some of it working better than others. But who cares what we have to say about it? What's your take on GemCraft?
For another look at the Freeware scene, check out BigDownload's Freeware Friday series.