Depending on what type of books they are, you can read them with any number of the free,apps available (iBooks, Stanza, Kindle, etc).
What I do is I have my Calibre library stored on Dropbox. Then, I can go to it, find the book I want and use the "Open In..." function to open a compatible app. If you don't have your books in Dropbox, you can drag them into iTunes le e-mail them to yourself. I also use a program called Calibre2OPDS that enables me to make a browsable catalog.
Hope some of this gives you some ideas.