I suppose it depends on the look your going for,
if you're just looking for a base to properly apply your eyeshadow and keep it from creasing, then a colorless base is going to work wonders.
But if you're using a base with a color to it , it's most likely going to show up somehow and effect the look of whatever you put ontop of it, but this is also something that a lot of people like to do. For example, when I put on Star Voilet, Swish, and Pink Freeze eyeshadows today, I used Overcast Shadestick, which is a white shadestick, as a base... mostly because I like the way it "frosts" out my eyeshadow colors. Also, I'll use Sea Me shadestick as a base for my lids if applying Freshwater or Fade eyeshadows.
If you're using a base that's nude and matches your skin, it's not going to effect the shadows.
Transparent, nude, and color bases all work great. It all depends on the look you're going for.
Hope this helps!!