How to compare two pdf files through command line

How about i-net PDFC - it does a full content comparison - text, images, lines, header/footer-detection and so on. You can use it either on command line or with a GUI (2.0, currently in public beta-phase).

The command-line tool already has the option to compare folders with PDFs against each other (or the extreme way: use the API ;))

Disclaimer: Yep, I work for the company who made this - so feedback highly appreciated.

Check out comparepdf:

comparepdf is a command line tool for comparing two PDF files. By default it compares their texts but it can also compare them visually (e.g., to detect changes in diagrams, images, fonts, and layout). It should prove useful for automated testing.

It is Open Source (GPL) and there are Windows binaries available.

Also:

If you want a GUI application that shows the detailed differences between PDFs use DiffPDF instead.