[Nook Color Q&A, Help & Troubleshooting] angomy:
Edit: I realized I rambled, so feel free to skip the long version below.

Short version: Not sure if you can ADB pull/push the paid B&N apps to another install, don't know how (if any) DRM works for that. While B&N apps are built specifically for the resolution, I find that they are very expensive (compared Angry Birds Seasons HD 99cents to B&N Angry Birds Seasons (HD) 3 dollars, and honestly I could not see a difference between the two) and if your Nook is not overclocked (which requires rooting), tend to be slow. There are some that are quite nice that I haven't found the equivalent of yet in Amazon App/Google Market such as Word Rainbow. You can find replacements/equivalents for most of the B&N apps in the other two stores I've mentioned. B&N sadly has a very small selection of apps that are actually any good, imo.

The native B&N reader app is far better than the Nook app (some functionality like enhanced children's books ONLY available on native app) and has not been, afaik, successfully ported.

Long, rambly, feel-free-to-ignore version pertaining more to ROMS than apps:

I've run unrooted stock, Manualnootered (rooted) stock, and various flavors of CM7.

- The native ereader app in stock has a very, very nice UI. Much better imo than the Kindle's. I still have to find a good replacement for it. It is also the only way, AFAIK, that you can read those enhanced children's books that lets you record your voice, or that has animations/reads to the viewer. If this is important to you, then stick to unrooted or rooted stock.

- Unrooted stock is so slow, that after having used overclocked rooted stock and CM7, I cannot bring myself to use it again. Even page turns were slow. App loading times are abysmal, and live wallpaper will not only eat your battery but cause everything else to slow down.

- Manualnootered stock is quite nice because you get to install 3rd party apps, have access to not only B&N's own store but also Google Market and Amazon App Store if you install them. You can also overclock so it's a much faster experience (highly recommended).

*Drawbacks are that there are some bugs that you may run into: Update issues with Adobe products, which cause boot loops (there's a fix for it). Not all apps may appear in Google Market (several things you can try to fix). And finally, if there's an OTA (over the air) update to the next (1.4, assuming you manualnooter to the latest 1.3 update), it will break your root/nootering and you will have to do it all over again.

- Installing a Cyanogenmod ROM: You get Gingerbread instead of Froyo (2.3.x vs 2.2.x), lots of goodies too many to list. With Tablet Tweaks (built in) and Nook Color Tools, you can tweak the bleep out of your Nook Color in terms of performance. You won't have to worry about OTA updates or the boot loop issue, but you do run into issues such as: "Your device is not compatible" messages when you try to install certain apps from Google Market (there are workarounds for most of them), SOD (Screen of Death, supposedly fixed with latest dalingrin kernel update), wifi issues (disconnect, difficulty connecting, etc.), force closes of random processes if using a nightly build. You could go with the stable build, but honestly the improvements in the nightly builds far outweigh the bugs which get ironed out pretty quickly.

The best part is, you don't even have to install just one of these. If you want, you can either a) dual boot stock + custom rom from EMMC (native Nook Color space), b) boot custom rom from SD install and keep unrooted stock to avoid voiding your warranty if you're concerned about that c) mix and match dual booting etc. It is pretty much impossible to brick your Nook Color.

After several months I've found that I prefer using CM7 builds simply because they are so much more customizable than rooted stock. I would suggest trying out both (stock, rooted or not, + CM7) via the SD card install + stock EMMC if you're not leaning towards one or the other.