I let my Nexus apply the 4.1.2 update last night, somehow not thinking about possibly losing root. Well, I lost root. Rerooting with WUGs toolkit left me with both SuperSU and Superuser installed. Apparently both apps get installed in /system/apps as Superuser.apk, causing confusion (with me, as well as forum threads I found elsewhere) as to how both are installed, and how to remove one without removing the other.
I found that updates to Superuser from the Play Store were the root cause (no pun intended), because they are installed in /data/app. I was able to remove Superuser (and keep SuperSU) by opening the app drawer and dragging Superuser up to App Info, and selecting Remove Updates. After rebooting, Superuser is no longer installed and does not appear in the app drawer.
I found that updates to Superuser from the Play Store were the root cause (no pun intended), because they are installed in /data/app. I was able to remove Superuser (and keep SuperSU) by opening the app drawer and dragging Superuser up to App Info, and selecting Remove Updates. After rebooting, Superuser is no longer installed and does not appear in the app drawer.