The method the pros use is to paint directly onto the mesh using a 3d painting tool.  Blender supports this, though the professional standard tool for this is Zbrush.   The technique unbroken-fighter mentions is useful if you want to map a photo or other image that already exists onto the mesh, but if you just want to paint in a more typical fashion, I don't think you need to do projection mapping.  I've never tried it myself, so I'm not clear on the details. There are a fair amount of tutorials on the subject, though.  Here's one on texturing and mapping (you can ignore the part about making a seamless texture since you already know how to do that).  Here's the Blender Cookie texture category, which should give you some solid nuts to bolts instructions to follow.  This Blender Cookie video specifically deals with the texture paint layer add-on, which you might find useful.

Photoshop also supports 3d painting from CS3 or 4 on (can't remember which).  The thing to remember when setting up maps and zones for this is that Photoshop will create separate images for each zone.  Mapping like V4's where there are several zones for one UV mapping and even one UV island will just waste resources. 

 

Edited to add: As NanetteTredoux mentions, projection texturing will still produce seams.  Just as in 2D, people seem to get rid of them by just painting over them with the clone brush and such.