The move to integrate ClockworkMod Superuser into CyanogenMod has generally been welcomed. The problem with the old super user apps (and there were several) is that they were all closed source. The new app is open source meaning that it can be subjected to independent security analysis. Before ClockworkMod Superuser, the reality was that every rooted device relied on the same bits of software to grant or deny administrator access and nobody was able to prove or inspect what these apps were doing! Although the chances of these apps being rogue was virtually zero, by moving to open source this has made it actually zero.
Other key features of ClockworkMod Superuser include multiple user account support on Android 4.2 devices, PIN protection and integration into the Android notification system. The app also supports tablets with an optimized user interface. If you aren’t using a nightly build of CyanogenMod you can get ClockworkMod Superuser from Google Play.