Originally Posted by unboggling
Pick one format, ePub or mobi, standardize on it, convert everything to it, consider it the master copy once it's cleaned up, delete any other formats, and generate whatever formats you need for various devices from that master on the fly as you need them. I now load my devices with only a few books at a time, the author or series I'm currently reading, and delete them from device when done. I add a content-rating tag to the book's record in my main library and delete those extra formats. Saves disk space and backup time. My "masters" are ePub rather than mobi even though my primary reading device is Kindle, because I noticed the calibre viewer opens ePubs faster, and calibre conversions seem to complete faster from ePub. [Edit: Per Ransom, html also is a good format to use for "master" copy.]
Even if you own a Kindle, ePub is the best choice for a master format. It converts easier to Mobi. It's easier to edit if you need/want to make changes. It means if you later move to a different brand reader, you have ePub read to go with you. There is no reason to use anything other then ePub as your master format.