Diff-PDF (click here to go to the download page) is a very useful command line tool for comparing pdfs. Only issue is that there is a lack of GUI frontend to use this. This is quite annoying for occasional usage of this program, especially for the average user.

Thus for anybody who really really needs this feature quickly, here is a good stopgap measure for those in windows. For linux users, it shouldn't be too hard to modify.

It is a python script that ask for two files via GUI and runs it in diff-pdf. To use it, just drop it in the same folder as the binaries, and execute the script.

#### GUI FRONTEND SCRIPT FOR DIFF-PDF (guiDiffPDF) ####
## Author: Brian Khuu 2014 briankhuu.com
## Description: This script will ask you for two files,
##              and then open a visual mode diff.
##              In other platform, just change diff-pdf.exe
## Install: Place in same location as diff-pdf.exe
##          Don't forget to put it in system path for handy access!
## Tested: On windows 8 with python V3.1
## Dependency: diff-pdf.exe @ https://github.com/vslavik/diff-pdf
import tkinter, sys
import tkinter.filedialog #https://mail.python.org/pipermail/python-list/2010-April/574512.html

programPath = "diff-pdf.exe" ## FOR WINDOWS ONLY, MODIFY THIS IF IN... SAY LINUX

## START GUI ##
root = tkinter.Tk()         # open and start tkinter object
root.withdraw()             # hide the root window
## save sys.argv arguments (As file dialog changes it...) ##
optArgV = sys.argv[1:] # optional ArgV.

## ASK USER WHICH TWO FILES TO COMPARE ##
filePath1 = tkinter.filedialog.askopenfilename(title="Open First PDF - 1")
print ("pdf1: "+filePath1+"\n")  #Display first filepath
filePath2 = tkinter.filedialog.askopenfilename(title="Open Second PDF - 2")
print ("pdf1: "+filePath2+"\n")  #Display second filepath

## Run the command line instruction ##
from subprocess import check_output
if ( len(optArgV) > 0 ):   # pass though argument to diff-pdf.exe
    print( "ARGUMENTS: "+" ".join(optArgV)+"\n" )
    command = programPath+" "+" ".join(optArgV)+" \""+filePath1+"\" \""+filePath2+"\""
else:                       # Otherwise default to visual diff
    command = programPath+" --view \""+filePath1+"\" \""+filePath2+"\""
print(">> "+command+"\n")
print( check_output( command , shell=True) )

input("Press Enter to continue...")

Posted the solution also to https://github.com/vslavik/diff-pdf/issues/14