If your PDF files numbered in numerical sorting:
Weenysoft Free PDF Merger — simply solution
I scan the book → I process scans → I get in output files: 1.pdf, 2.pdf, 3.pdf, …, 4147.pdf. I need preserve the order: 1.pdf — page 1 of merged PDF, 2.pdf — page 2 and so on.
But use tools from section «Not helped» I can't do it ...
You can probably get it done with Pandoc, as its description is exactly what you're looking for:
Pandoc can convert between numerous markup and word processing formats, including, but not limited to, various flavors of Markdown, HTML, LaTeX and Word docx. For the full lists of input and output formats, see the --from and --to options below. Pandoc can ...
For the ones that is hosted on your own server and you embed the flipbook within your site, you can use dFlip PDF FlipBook jQuery Plugin.
It is flash free. Costs only $29 for regular license with 6 months customer support. You can create 3D or 2D flipbooks easily with this plugin. Additionally it has awesome page rolling effect.
You should definitely take a look at PDFtk pro & server. (The pair will cost you $3.99).
The pro edition is a GUI that allows a lot of control
The server edition is the command line back end of the pro-edition.
They will allow you to:
Merge PDF Documents or Collate PDF Page Scans
Split PDF Pages into a New Document
Rotate PDF Documents or Pages