I prefer to assemble everything of a particular color and paint it as one assembly. For aircraft I assemble the entire fuselage including wings, ailerons, spoilers, empennage, wheel bay doors, etc. and paint that as an assembly. Sometimes you can't do this though, it varies from one model to the next. I don't like painting individual parts prior to assembly because I wind up ruining most of the paint trying to get rid of seams where they go together.