Some questions regarding apps on a rooted Nook Color
A vast majority of it. My device says I have up to 5gb of internal storage that I can use. Additionally you can throw in an SD card.
In my experience about 98% of the apps on the Market will work on your rooted (stock) Nook Color.  If you flash CyanogenMod 7 or similar, then they all should work.  If you remain with stock, there are some minor quirky issues because there are a few things missing from the OS.  For example, trying to create a "shortcut" will cause a Force Close.