I paint the bases of all my miniatures in a colour according to the faction they belong to. I'm not sure about the Shadow miniatures with the crossbows. Are they Sauron units in both games, or Isengart units in the Rohan game and Sauron units in the Gondor game? In both cases I'm referring to the background (the books).
Hmm, I think I rather leave their bases untouched. All other troops (except ships, catapults, siege engines) have painted bases, so they stick out anyway. I love the games, but I'm not going to buy second copies till something is damaged or worn-out.