I tried a bunch of launchers when I first rooted and finally settled on ADW. For me it was easy to set up (once I got over the "I don't know anything about Android" feeling) and I initially used the selected app screen as my "Home". There are two ways to do that. One, after installing ADW and rebooting the Nook it will ask which app you want to use to open "Home" and you will have a chance to set that one as default (either the B&N stock Home screen or the ADW app drawer). And/or, you can use NTMM to assign the QuickNav "Home" button to ADW Launcher.
Pretty much any launcher should provide you with the same options once installed when you reboot.
So that's what I used to do but I eventually went back to the B&N "Home" screen on boot and then after that I can access it from a long press of the "N" button (again, you can assign that with NTMM). I've almost completely reassigned by QuickNav buttons (except for Library). See this
post (result in #4).
I've also done the multi-touch enhancement (nice for Opera Mobile and some other apps), No-Refresh and FastMode2 (contrary to what the posts seem to indicate about FastMode2 I have found that the app does indeed toggle the mode on my NST so I assigned it to one of the side buttons and No-Refresh to another one).
Lots of info on various apps out there. Here's my "short" list of what worked for me (in no particular order):
Cool Reader (I only use this to set the screen saver to my current book!)
Amazon Kindle (the enhanced version posted elsewhere on XDA)
Orion PDF viewer
ES File Explorer
Places (Google Maps variant)
Email (gave up on Gmail--this app is found in another XDA post as well)
Those are on my ADW home screen along with the GenieWidget for local weather and a widget for Clean Master. I've divided the app drawer behind the home screen into two categories, "everything" and "utilities" which is where I leave my focus and there the following are found:
No-frills CPU Control
Nook Touch Mod Manager
No Refresh settings
Search Market (got rid of Amazon Market which was giving me a lot of trouble)
WiFi File Transfer
Other apps that hide in the "everything" section because I almost never need to access them are:
News and Weather (Genie Widget)
I also did the triple Flash installation described elsewhere but it really only works with SWF files as far as I can tell and only with Flash-able browsers like Dolphin (which has other issues). And I did a Framework-res.apk mod to slightly grey the backgrounds of menus so that some of the "invisible" menu options that come with many apps can actually be read).
I don't know how many times I've made backups and redone things, trying to find what works for me (mostly reading, some browsing). My Nook is still fully B&N functional, as far as I know. The only thing I have not tried is logging on in the store. Except for the inadequacy of Opera Mobile (I've tried every other browser known to humans and aliens), the set-up actually is pretty nice