Dark means that you are getting concentrated skimmate. If you skim "wet" then you get a lot more liquid but it isnt as concentrated with the things that you want to remove. Skimming wet gets more pollutants out of the water, but it takes a lot more tank water with it. In that case you need to replace all the water and salt that goes out in the skimmate as well as change it every day. If you skim "dry," then you get a much higher concentration of crud out of the water. As long as your skimmer is rated for your tank you're still getting enough crud out of the water, and you have to do a lot less work replacing water, salt, and emptying the cup.
Also, you feel kind of bad-*** when you get a really thick skimate.