Ed Elliott has another nice tool in his SSDT Dev Pack:
This new tool for the SSDT Dev Pack adds a menu item (Tools–>SSDT Dev Pack –> Find Duplicate Indexes) what it does is scan all the projects in the solution (it doesn’t follow “this database” references to examine them, maybe a future version) and then print to the output window a list of all the duplicate indexes based on the table, the columns and included columns – I don’t check anything else so you might actually want a duplicate in some circumstances but these should be very few and far between.
If you double click on the index it will take you to the location in the code where it actually is so you can delete it 🙂
A very useful tool gets even more useful.