Meshmixer is a very peculiar bit of software. It makes it very easy to combine existing objects, but it does so in a unique and intuitive way. This video explains it much better than I ever could;
What makes this amazing to me is how easy you can just 'drag' an object over another object, and it'll follow the shape wherever it can. The connections between the two objects are also quite smooth and natural.
It looks like Meshmixer is doing a good job at generating manifold objects - as long as you input manifold objects, that is. I ran a few tests and each design was printable by Shapeways. The current version only loads .OBJ files, so you may need a tool like MeshLab to convert your files.
Meshmixer is developed by Ryan Schmidt, a computer graphics researcher at the University of Toronto. It's a free, Windows-only download.