I can't remember which rooting method I used, but there were a few apps added to the Extras link, including the Market. Ok, I looked up some information and I used the full AutoNooter method.
http://forum.androidcentral.com/barnes-noble-nook-color/54069-guide-rooting-your-nookcolor.html
You can also find very good information at:
nookDevs
Look at their Nook Portal for the best information.
Finally, both of the above links, will tell you to download Win32DiskImage.exe. That is NOT the correct name. You need Win32DiskImager.exe (note the additional "r" in the name). It is FREEWARE, so don't download it from a pay site as it will probably be a trojan or something. I downloaded it from here:
https://launchpad.net/win32-image-writer/+download
You can also get one from here:
https://wiki.ubuntu.com/Win32DiskImager
There ARE some quirks to using the NC post rooting. At first blush, it looks just like it did before, except you have a few apps in the Extras that weren't there before (UPGRADE to NC OS 1.01 BEFORE you root!). One of which is the Market. When you install apps from the Market, you (at least *I*) have to power down/power up the NC to see the new app(s) in the Extras screen.
There is also an app that puts soft buttons on the NC so you can click menu, home, back, search on screen. It is pretty nice if you, like me, are frustrated by not being able to go to a previous screen without having to retrace your path from the main NC home screen.
Using an app like Home Switcher AND another home app like Launcher Pro (or ADW and others), you can switch back and forth between the native NC home screen and Launcher Pro. The caveat, which keeps me from using Launcher Pro as my default home screen is that I cannot figure out how to access the native NC reader app from Launcher Pro.
Anyway, IMO, it is definitive step up from just having the NC as a reader. It also allows you to install better media players for video and music. Hey, you have access to almost all of the Market apps. Even Angry Birds, which both looks and plays GREAT on the Nook!
Oh, and if you are planning on watching .mp4's, I would strongly recommend against using the NC app. Get one from the market that doesn't rely on the native Android player (I THINK RockPlayer is one). That way you can run it either as software or hardware. I haven't tried any music apps like WinAmp yet, though I plan to.
The downside of rooting, well not a function of rooting is that some of the apps don't work the way you expect them to, especially games (such as Hungry Sharks, it won't play wide screen, so some of the right and left of the screen is cut off). However, there are some nice lists of apps that do work on NookDevs.com.
At the least, you are enabling more functionality in your NC. At the best, you are getting an almost fully functioning Android tablet for $250!
Scott
PS. Disclaimer: As with anything like rooting, there is the chance you might "brick" your NC. I haven't personally heard of anyone actually doing this with the prevalent AutoNooter, but it COULD happen.