From
http://calibre-ebook.com/user_manual/faq.html
"What are the best source formats to convert?
In order of decreasing preference: LIT, MOBI, EPUB, HTML, PRC, RTF, PDB, TXT, PDF."
But you may find this order isn't exactly right if you are converting a number of books with particular properties, like academic journals or something like that, so experiment. Lit books are great, for example, but some I have converted have footnotes at the bottom of every page which is very disruptive to read in a small format like a Sony Reader. But in an IPad or tablet computer, it might well be just great.
The creation of a 1000 books starts with a single conversion.. Have fun!