Not sure if this will do everything you want but is sure comes close.
It is a free program called allwaysync found at www.allwaysync.com
It is a directory sync program but you can invoke filters to get just the output you want ie non-duplicates. You can then tell it what to do with the files and/or do nothing if you are just comparing. Very powerful. Can see if time/date stamps match ect.
Allway Sync Features
Free for personal use synchronization software. No spyware, adware or malware.
Easy-to-use graphical interface.
Performs true bi-directional and n-way file and folder synchronization, forget about backup and restore routines.
File modifications and deletions are tracked in a local database. So, Allway Sync knows the true history of your files - no unnecessary questions asked.
Our innovative, proprietary algorithms do not rely on the accuracy of the system clock or network connection quality. So, Allway Sync helps prevents data loss.
Generates a full report of differences between synchronization folders.
Synchronizes folders as well. Allway Sync detects when folders are removed from one device and removes them from any other corresponding synchronization targets.
Supports virtually any file system (FAT, NTFS, SAMBA, Netware, X-Drive, CDFS, UDF and more).
Can be installed on a desktop, laptop, USB stick, external HDD or a U3-enabled device (see details).
Capable of synchronizing more than two folders.
Synchronize data between your desktop PCs and laptops over a network.
A good way to backup and restore files if you run Allway Sync in one-way mode.
Specify independent synchronizarion parameters for any number of sets of folders (multiple jobs).
Transfer documents from one computer to another using an intermediate removable drive.
Or just synchronize with a removable device (USB key, flash drive, CDRW, Zip) so that you always have your data with you.
Flexible configuration and customization.
Supports files of any size.