Towards the end of February Koushik Dutta, best known as the author of ClockworkMod Recovery, released a new superuser access app called ClockworkMod Superuser. The initial release could only be installed via recovery mode but it didn't take long before it was made into an .apk and uploaded to the Google Play Store. The popularity of the new utility, which allows users to grant and manage which apps have root access on a rooted device, has been phenomenal (considering it only applies to rooted devices) and now ClockworkMod Superuser has been fully integrated into CyanogenMod.
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.