I like using Windirstat. The big problem, at least for me, is that even some bad and/or short games take up a bunch of hard drive space, and I haven't found the size of a game to directly correlate to its quality. So when I want to spring clean my drive, I use a free disk usage analyzer (like windirstat) to see what's taking up the most space and figure out if I'm still playing it, if I left a big redundant zip file after extracting it, or have multiple versions of the same game cluttering my disk.
But if it's just the sheer number of underplayed/bad games that bothers you and (somehow) not disk space, then it's probably smart to delete whatever games you don't play one by one and, if you're really tidy, make sub-folders for different game genres.