So what happens if a bug slips into Superuser? Well, you can't update your ROM in ROM Manager. You can't remove bloatware with Root Explorer. You can't overclock with SetCPU. You (essentially) aren't rooted.
And unfortunately, the latest version of Superuser (v3.0.4 as of this writing) has a bug in it.
If you notice a force close popping up every time you try to open a rooted app, this bug is the reason. Now, Superuser is a great app and I'm certain the bug will be fixed in no time, but until then, it kinda sucks.
But luckily, Android genius ca1ne pointed out to me today that there is a temporary fix. In Superuser, press MENU > Preferences > Automatic Response (first option) > Allow (third option). This will allow Superuser to automatically let your root apps get the permissions they need to run.
From my experience, you may still see a force close. But everything is working like normal again.
Oh, and if you're worried about some bad app getting root permissions without having to ask, a notification will pop up whenever an app gets a permission (and Superuser tells you where it's from). So, if you see a weird app getting root permissions, then it's probably time to uninstall that weird app.
Update: The newest version of Superuser has fixed this problem.