I have found that many people are not PC savvy enough to copy books to their Kindle. Most people can not create collections and organize their books.
Enter the Kindle Collection Manager.
I had settled down to write my own version of iTunes for the Kindle and started doing research on the Kindle’s secret file structure. What I found was this short and sweet little file manager. There is no need for me to write anything when The Kindle Collection Manager works just fine, is free, and doesn’t include any malware or nagging messages.
The Kindle Collection Manager allows you to create collections (by right clicking), and then you can drag and drop the books to the new collection.
The only thing missing is the ability to drag and drop MOBI files to the Kindle. I am suggesting this to the author.
The Kindle Collection Manager. The Windows app for your Kindle.