I would start by putting the indexes into a spread sheet grouped by tables. Start by comparing the order of the equality columns (your WHERE or ON clauses would be using Column = value for these), then look at the inequality columns (column >= value or such in a WHERE clause), then look at the included columns.

I have had the missing index DMV and DTA suggest adding an index with 40+ included columns from a table with around 50 columns.

This is just a quick jump start. Even after you narrow down the indexes, you really need to test them in a test or development environment before putting them in production.