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The most capable appears to be Rhino. You can model and unroll, though I'm not sure in regards to coloring. Fairly high price point and learning curve. Next would probably be Sketchup. Modeling, and a plugin for unrolling, again I'm unsure as to coloring and I believe the full version is also several hundred dollars though the free version appears to be used by a number of people. Less steep learning curve, though. In free open source areas there is Blender for modeling and again a plugin for unfolding. Steep learning curve but no price point at all.
There are quite a few options if you want to model in one application, unfold in another (few options to do this really) and color in a third. It's the unfolding functions where your options are limited. Pepekura seems to be the most used. There are a lot of different modeling options out there, both commerical and open source, and most of them will save to *.obj format which can be imported into Pepekura for unfolding.
For the coloring it depends on whether you want to work in raster or vector formats. Again, there are a number of commercial solutions but open source provides GIMP for raster and Inkscape for vector. I think they rival the commercial competition but it really depends upon what you're comfortable with.
Much of it also comes down to how complex your model is going to be. Unfolding is the bottleneck. The more complex your model, the less likely you will be at using the simpler solutions. Sketchup, Blender and Pepekura all seem to have challenges with complex models. To me, it seems very easy to get seduced into believing that a detailed 3d model will make a great paper model. But it is very easy to make your 3d model too complex to unfold.
--jeff
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