I rooted my stock and it is VERY easy. You just follow the very simple instructions to prep your nook and to download a file onto an SD card then place that SD card into your nook while it is OFF and then boot it up.
The advantage of the rooting is basically so you can
1) Get the Android Market
2) make changes to the user interface to make it more customizable.
The reason you may want the android market is for additional functionality. Basically with the market you can download any app you need to gain the functions you want. This is REALLY what sets an e-reader apart from a tablet. Do you need to take notes for work and it would be nice to do that on the e-reader? Plenty of app options for that (I use evernote). Do you want to transfer itunes music to your nook? A couple apps will do that. Want to put some pdf or doc files in a folder on your comp and have access to them on your nook to read on the couch? Dropbox will do that. These are just a few of the apps you can get out of the android market to increase the functionalities of your nook.
As for the increased customization of the UI that gives you a lot more control of your user experience. I use a launcher (kind of like a theme for windows with much more flexability) called Zeam that allows me to utilize one of my favorite things about the Android platform Widgets, which allow me to place things right on my home screen to give me immediate access to functions and info on my nook.
So that is the advantages of Rooting the stock Nook ROM (os).
Now some people are putting the updated Android OS Honeycomb (HC) on their nook. Currently this is a version of HC derived not from the full HC release but from a preview version released so that app developers can test their app functions (as I understand it). The advantages of this version of the OS is that it is INTENDED to be used on tablets (All previous versions of Android, including the Eclair that comes standard on the nook, are really an OS optimized for cellular phones) and so it has some tweeks to the way it works so that it is better for tablets. Some of these are simple little things like button placement. Android is optimized for having access to 3 or 4 buttons (aside from power and volume control) all the time. On most phones these are hardware buttons located just below the screen in portrait mode. If you shift the phone to landscape the buttons are still there on the side now, but a phone is small so this is no big deal to work with. The nook has 1 button (aside from the power and volume control) and the rest of these buttons are software solutions on the bottom of your sreen (the little back button that pops up there sometime, and the option to access you "library" and "extras" from your nav menu). In Honeycomb these buttons are software buttons that shift with the orientation of he device. This is nice for navigation in landscape mode and in portrait. That is one of the many little changes in HC that make it run better and be more usable for this form factor (though I think B&N did an excellent job making this form factor useful and with Softkeys, a software solution for those missing buttons you can use in SOME full screen apps that block access to the B&N options it is perfectly serviceable). There are some caveates to HC right now. It is not 100% fully baked right now and so somethings don't work exactly right. That is because it isn't made from the full download of the code for the operating system yet. A 100% baked HC should come in time but for now if you are like me, a rooting/hacking novice the best most stable way to go is to root the stock ROM and use it. It is very easy and very user friendly once it is done.
I hope that helped some.
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