Index Usage

The key is, you don't want to just know which indexes are "used," but how they're used. Looking at sys.dm_db_index_usage_stats will tell you if your indexes are getting scans or seeks. In general (and there are exceptions to this) you want to see seeks. But, you really have to evaluate not simple how many times an index is touched, scan or seek, but which procedures are calling them? You may have a query that's called once a day, but by the CEO, you might want to leave that index. All looking at the DMO will tell you is, if the index is used. You still have to do all the research around how, by what, when. Then, before you drop the indexes, you need to test your code to validate it's not negatively affected when you drop them. It's a huge job.

You can start by checking out Brent Ozars Index Tuning for SQL Server video and scripts.

In addition to the other answers, I would like to recommend you should also to take a look at the singleton_lookup in the sys.dm_db_index_operational_stats. That will give you an hint if you should alter one or more indexes to avoid costly key lookups, by creating covering indexes or even change the clustered index.

But as you already know, it's a heavy investigation project, so you should go for low hanging fruits to prevent the worst performing queries.

You can try to find the worst performing queries by using sys.dm_exec_stats and get the cached execution plans from sys.dm_exec_query_plan where you actually can find the used indexes.