What should be the result of the comparison? PDFs contain text, images, formatting information, watermarks, digital signatures, forms, document meta information, etc. Which of these do you want to look at?
In general, it's not possible to access information in PDFs. Some tools let you extract their text (e.g. JPedal), but that's about it.
There's a hole in the bucket, dear Liza, dear Liza, a hole in the bucket, dear liza, a tiny ad: