i store mine alphabetically and by type (kisser slickers together, liquid together, vegan together, etc.). When I was hard on space, i bought a bulk pack of marker clips (basically what comes with a dry erase board, but by itself- i bought a pack of either 100 or 200 i think but you don't have to buy that many) and stuck my lippies to the wall (mine was inside a closet, but you could do it on a door like the back of a medicine cabinet door).
Some people put dots of nailpolish on the cap, but i just don't have that much nailpolish. If you do, you could try it. At the very least you could probably mark red, purple, pink, light pink.
The only other simple fix i can think of is to print out a color scale:
http://www.creativeuplink.com/htmlbgcolors.png (like the listed cheat sheet for html color codes), cut out the little squares and glue them to the appropriate cap.
i did like the clear tube truly came in...
i could be wrong but i imagine most lip tube packaging is sold as a two-piece set (tube and cap). It might be hard to buy JUST the caps...