I got this one from Jason's Blog.
Paul O'Brien, a Microsoft MVP for Mobile Devices and MoDaCo network Founder wrote this neat application - DupeDeDupe - that allows you to remove duplicate contacts from your mobile device. It works with Windows Mobile 5+ and Pocket PC.
"It is an EXE only (copy to your device and run), which has a basic GUI which allows you to scan for duplicates, and then choose (after being told your duplicate count) whether to remove them. Contacts are compared based on 'File As', field, 'Email' field and 'Home / Work / Mobile' phone fields. If all those fields match, it's deemed a duplicate."