It's good to have a variety of colours in the collection, but if I had to really pick one; I'd go blue, white and red. It looks heroic/patriotic, and it feels like the right mix of cool and warm colours. I can understand why many people go for black, but if you had a shelf of Transformers and nearly all of them were black, it'd be a bit creepy looking
Another interesting thing about colour schemes (in Transformers) is that purple and green seem to be associated with evil. You almost never see Autobots (or superheroes in outside media) sporting purple and green. The only one that springs to mind is the EVA unit-1 from Neon Genesis Evangelion, which was piloted by the main hero. Besides that, no "good" characters seem to like wearing those colours.