Organized iBooks?

It's gonna take a lot of time and elbow grease to fix it. All the meta tags within the "Get Info" area for each book has to be accurate. Right click each book and select "Get Info". Correct each title and author in the sorting area. It's a slow process.

 

I make sure all my books are tagged properly - either using iTunes or Calibre. Then I organise books into collections.

The two default collections are Books and PDFs, but you can add others. (Just tap Collections and then New). Examples of other collections in my iBooks library are American Literature, Biography, Contemporary Fiction, Non-Ficton, Crime & Thriller, Sc-Fi & Fantasy.

 

Calibre can add metadata automatically

You can easily manage your ePubs and PDFs via calibre. For each ePub or PDF, provide a ISBN number (or Amazon asin number) and calibre will fetch the book metadata & cover art. Calibre also integrates well with the Stanza app for iPad to browse your collection of books.

Also, if you're reading PDFs on an iPad, using iBooks or other app, you can attach a table-of-contents to the PDF using an app like PDFOutliner ($5 on the mac app store) to quickly navigate inside the PDF.

disclaimer - I'm the developer of PDFOutliner