Organization is one purpose of cubes. But you can also use them in less than clean hotels/hostels. You can pull them from your suitcase and put them in drawers in your room, not having to worry about your fresh clothes coming in contact with who-knows-what.
Weight, as mentioned, can be an issue. In these cases, I find simple grocery plastic bags or Zip-lock bags more appropriate. Clear Zip-lock bags also let TSA screeners see better what's in the bag. Don't know if that has any tangible value, though.
Compression bags can be useful too, but stay away from those that are evacuated with a vacuum (often hard to come by at your destination when preparing for the return trip).
Bottom line: I usually travel with a combination of cubes, plastic bags and Zip-lock bags. I think it's good to have a basic set of cubes. I like both the ones from EagleCreek and the ones from eBags (along with their shoe bags).
Cheers! MM