As a rule of thumb, it is usually best to add indexes only to solve a specific performance issue. If they solve the issue, they are useful.
I know this isn't a tool, but it is an approach to your problem that I would expect to work better than a tool (assuming someone is able to suggest one - which they haven't yet).
Indexes are also not all positive. Adding one MAY speed something up, but it will also DEFINITELY slow down inserts, administration, and utilise additional disk space.
My suggestion then would be to take off any that you aren't sure are serving a purpose, and experiment with any that you think might.