I researched ISBN for our small company that has 6 printed books in continuous print for > 20 years and now we are doing the eBooks ourselves. In USA Bowker (
http://www.bowker.com/index.php/bowker-brands/bowker-isbn) is the only source of ISBNs, however they authorize others to be re-sellers as well. The website and direct calls to them was much of my information as I found, like this thread, conflicting "facts" and info/opinions online. Of course, Bowker is motivated to sell more product (ISBN) as well as their newer product DOI (Digital Object Identifiers).
Like some have said here, the official guideline from Bowker: same content/title but different output mobi, ePub, PDF would each have a different ISBN. I can't remember the online eBook outlet that indicated in their FAQ that they wanted the above followed, but then in looking at what they actually allowed to be for sale from both their best selling to low sellers, they did not enforce this rule.
Our own company still has close to 900 ISBNs from block of 1,000 purchased decades ago so we can afford to use them up, but decided to use one ISBN per eBook title. We figured that anyone who is about to download an eBook would see on the same online retailer page all version types available from that outlet and would choose appropriately. If someone were citing our non-fiction book in a footnote or bibliography and including the ISBN then someone else using a different eBook version would not be confused if they saw their own eBook having a different ISBN. This is probably a non-issue for works of fiction, but not necessarily so.
Earlier poster had asked about difference in 9 digit and 13 digit ISBN numbers - as far as I know at least in USA there are only 10 digit ISBNs that were given the identical 978 prefix starting in 2007 to make them 13-digits in length.
The following is from Bowker.com FAQ:
All ISBN-10s officially changed to ISBN-13s on January 1, 2007. This has been accomplished by prefixing all ISBN-10s with the Bookland EAN prefix '978' (not '979') and recalculating the check digit. '978' can be thought of as the area code to which all ISBN-10s belong. All ISBN-13s that begin with '978' can be presumed to have corresponding ISBN-10s. This logic allows trading partners to readily translate between ISBN-10s and ISBN-13s.
While no one has mentioned it in this thread, according to Bowker there is no such thing as an EISBN or eISBN;
there is only ISBN that would appropriately be used on printed books; eBooks; sheet music; etc. While the prod decscription for an eBook now less frequently lists eISBN in outlets that I visit, this not-according-to-the-rule-book practice can still be seen.
ISBN is completely independent of copyright, although it might serve as some support if there is copyright infringement on your work. Unfortunately depending on the nature of such copyright infringement and how much of a loss it is to you, the cost of pursuing things legally can outweigh the potential benefits.
As someone indicated in earlier post, having ISBN on your work might be a good business decision, and for some outlets might be a requirement. In my opinion, if your author name is not particularly unique, having ISBN from legitimate source gives a unique identifier to your work. I believe it was here that someone mentioned purchasing "recycled" ISBN numbers. For me this seems like a red flag. Unlike telephone numbers which do get recycled, according to my information from Bowker there is no such thing as a recycled ISBN number. It is owned by one person who then can assign it to one work in perpetuity.
13 digit ISBN the 978 indicates item is from book publisher
2-digit group identifier e.g. 0 or 1 for English speaking
4-digit publisher code
The above 9 digits would remain constant ... followed by 3-digit for the unique title
The 13th digit is a check digit that is generated by a formula using the previous 12 digits, and makes sure that certain errors in ISBN are not present, e.g. if correct ISBN contains 766 but had been transcribed as 776; or if it contains 2374 and were transcribed as 2347.
Hope that some of this is helpful.