I have about 1500 side-loaded books on my nook (classic). My library on my desktop is organized using calibre. I use a program called calibre2opds to move both the books themselves and also a catalog from my desktop to the microSD card in the nook. From there, I use a program called trook to access the catalog. This gives me great navigation through the library. View by author, by title, by series, by date added, etc. All with a multi-level hierarchy that is easy to understand (think card catalog or phone-book metaphor for each of the various views).
rooted nook classic + calibre + calibre2opds = reader's nirvana!