The Kindle reads DRM-free (no encryption) MOBI ebooks from any source. However, many ebooks have DRM. Just about every other ebook site uses the ePub format. B&N uses a password-based DRM, but most other sites use Adobe DRM. The Nook can read B&N and Adobe DRMed ePubs, but it prefers B&N ebooks.
It is very easy to strip DRM from B&N and Adobe ePubs. One good source of information on such things is Apprentice Alf's Blog. It is probably legal in the US to strip DRM from an ebook you bought if you are doing so in order to read it on another device. The Kindle does not read ePubs, but DRM-free ePubs convert nicely to MOBI using Calibre.
My advice is to keep the Kindle and buy most ebooks from Amazon but also buy from other sites if they have a better deal or an ebook missing from the Kindle store.
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