[KryptoNyte]

spm, just a few things to note (my lay person's understanding anyways):

1) Superuser - it's my understanding that some apps require access to specific system files, files that normally wouldn't be accessible to just any application. When an app attempts to access these files for the first time on a rooted system, it will usually ask you if it's okay to do so. I liken it to Windows Vista user access control constantly asking for permission to do something. Most of the apps that folks speak about here on this forum are trustworthy, as far as we know, and we generally give them superuser access when requested. If you fail to do this, it's very possible that the app will never operate properly.

2) Newly rooted folks - the one thing that you are probably going to want, if you haven't already found it (I gather you haven't as your desktop probably doesn't look much different than it did prior to rooting), is a "launcher." There are a few good ones, but I know that many of us use ADW.launcher (the free one), which can be downloaded and installed from the market. Your NC needs a launcher when it starts up to show some kind of desktop, as if Android is missing this from the start (like starting up Windows to a black screen and no function = no launcher). Once you install the launcher and reboot the Nook Color, upon your next bootup, the device will ask you which launcher you want to use, the default B&N, or ADW, you would want ADW (and check the box to enable this as the default). I was originally new to Android and didn't know that a good launcher really makes the device.