Recently, I bought a brand new Kindle Paperwhite and I am very surprised with it because it just works on Ubuntu in transferring ebooks. So far, I have three different methods to transfer ebook to kindle from Ubuntu, there are transfer via Calibre, direct transfer from file manager, and make use of send to kindle email service.

1. Transfer via Calibre
Calibre is a opensource ebook library management which has many abilities such as managing ebook collections, converting ebook, sync to ebook reader devices such as Amazon Kindle, download news from the Internet and convert it to ebook friendly format, and more.

To use Calibre to transfer ebook to your Kindle device, please install it from Ubuntu repository, "sudo apt-get install calibre" should do that for you. Once installed, run Calibre and plug the Kindle devices. Calibre will automatically detect the Kindle and you are ready to go!

Once connected, you can add and remove ebook from Kindle, and also convert unsupported format into Kindle supported format.

2. Direct transfer via File Manager
If you don't need a complex method of transferring files (like Calibre does), you can transfer ebook via File manager. Please make sure there is no ebook manager software opened, plug in the Kindle, and File Manager should mount it automatically (like Thunar - XFCE File Manager - does).

All you need to do is put the ebook in "documents" folder. Please make sure that the ebooks you put in is supported by Kindle.

3. Make Use  of "Send to Kindle" email service
If you have a good Internet connection and the ebook is not over 25MB (not too big for email attachment) you should use this method. Using this method has some advantages such as your ebook will be kept in the cloud and Amazon can convert the ebook if you want to.

Send the ebook as attachment by using approved email address to send-to-kindle email address, if you want to convert ebook to supported Kindle format, please write "convert" as the subject of the email. Please note that Amazon can only convert Microsoft Word (.DOC, .DOCX), HTML (.HTML, .HTM), RTF (.RTF), JPEG (.JPEG, .JPG), Kindle Format (.MOBI, .AZW), GIF (.GIF), PNG (.PNG), BMP (.BMP), PDF (.PDF) files. For further information about Send to Kindle email service please click here.

Regards :)