You can only open two file types on the iPad in iBooks, and they can not have DRM (Digital Rights Management), also known as copyright protection.
If the files do not end in .pdf or .epub, iBooks will not recognize them.
The Kindle app uses it's own azw standard, though you can side load .mobi books and pdf files. However the Kindle app will not appear as an Open In option. You have to side load the books through the Amazon site or using File Sharing in iTunes.
Most other third party eReaders also use the epub standard. Which is about all I can tell you about them.