What i like the most about Calibre is that it has a very simple interface that anyone can use, and it also can convert many of the popular formats such as PDF and EPUB with just a couple of clicks. It even searches a database that will help tag your files as well as find cover art and creates a separate file so that you can keep your original file and upload it to your device.
If you are using any iOS device (iPad, iPhone, iTouch), just open iTunes. Go to file, select add file to library, sync to your device, and that's it. The best part is that Calibre is free and is available on Windows, OSX, and Linux.
Below is a quick guide tour from the creator of Calibre. For more information, visit the homepage for Calibre: http://calibre-ebook.com/