Very good point. Calibre is an excellent piece of software (much better than ADE to my mind) and good at converting books, eg to Kindle format.
Unfortunately, Calibre will not handle DRM books (neither Adobe DRM nor Kindle format DRM), which rules out almost all bought books and library books.
You can go via a DRM stripper such as epubee. The exact legal boundaries of drm stripping are unclear and vary from country to country, but from everything I have read it is legal for personal use in the UK and US. It may violate the t&cs under which the books were sold.