I've been looking for a thread on the best ways to organize collections in Kindle 4 but no luck so far. Hope my post will be useful for this thread.
I use
ICE Book Reader Professional to read books on my PC. The program can sort books by author, then series, then the title. You can add notes and it has some other things that allows users to easily find a book.
Unfortunately, Kindle 4 NT is very limited in that respect. Kindle Collections feature does not support book series AFAIK. After a day of frustration I overcame that restriction.
Now my books inside a collection look like this
The name of the collection is the name of the author of all the books inside the collections. The book series you can see on the right side are actually author names in metadata fields of a specific book.
I exported my books from ICE Book Reader, imported them to Calibre, converted to MOBI format, copypasted via USB to Kindle, and created collections using Kindle Collection Manager.
The trick is having Calibre treat the names of book series as book authors during import and exporting converted books into a book author folder. After that Kindle Collection Manager can easily create a collection named exactly as a specific folder.
It won't be as handy for those, who already have set up their collections but it may give a hint to anyone, who wants their books stored a bit better.