Just recently I completed my first ebook/report (only 12 pages) that I'm giving away on my related websites. Like most others, it's PDF. I personally prefer Desktop Author, but since PDF seems to be the standard for quite some time, I will go with that format.
I don't like distributing other people's works with all the obvious backlinks to their offers and products and I'm sure a lot of others also prefer not making others rich, so my ebooks will be only informational to the reader, with no apparent backlinks.
BUT.... buried within the text, some of the relevant keywords ARE linked back to my websites. What I did, was remove the underlining of the link, and change the link color from blue to black. I created the ebook in Office (MS Word will work too), because it allows me to easily "export to PDF."
Now, I have an ebook to freely give away on my sites (they're all the same broad niche) with invisible backlinks to my sites. In the ebook I state that the ebook may be freely distributed. I want to do it, not to use the books to sell anything, but just to offer free information on my topics and to get free backlinks.