I use Netfabb a lot. Although I'm using the Pro version, its very similar to the free version. For the kinds of repairs the free version can make, I recall it seemed to work fairly well.

However, I'm often chasing my tail with fixing intersecting triangles in the Pro version. Starting with good topology is definitely the key. If you are printing your own models then you can construct them in a way that they will be printable (usually).

I get lots of files made by others and have to fix them for printing. I'm starting to experiment with retopologizing.