This was something of a challenge with my current army, a Horus Heresy force made up from the survivors of the 3 Loyalist Legions present at the dropsite massacre, the Salamanders, Iron Hands and Raven Guard. The problem was making each Legion look distinct, but also tying the force together so it looks good on the tabletop. Thus far, I think it's gone rather well, and there's a few things that have helped there,
1) the style/tone is kept consistent across the force. Everything has heavy weathering, applied in the same manner regardless of base scheme, and that does a lot to provide a coherent element to the army. Likewise, elements shared across all 3 schemes are kept similar; all the metallics, eye lenses, pouches and holsters ect get done using the same methods. The overall look is also very dark, so the disparate colours don't clash as much as if they were more vibrant.
2) The basing is also kept the same. The bases are really nothing fancy, just black rock and mud, but having these separate schemes stand together in one squad is really sold by them all standing on the same ground,
Here's a couple of examples. Apologies for the blurred pics (my camera does not liking photographing more than one mini at a time!

) but you can at least see how those elements keep it cohesive. In this case it's within squads, but the same elements apply across the army.