For independent baronies: check the ledger (button in bottom right) for "independent realms" and look for the ones with realm size = 1.
Holy orders are often to blame for this - again, you can look for them in the ledger and check that they don't have any baronies. Alternatively, if you can remember the names of all the holy orders, you can check each one individually using the title finder (again, it's a button in the bottom right).
If that doesn't give you an answer: loop through every independent realm (you've conquered most of the world so there shouldn't be too many); select its current ruler; check the yellow glowing outline on the map (if a realm has a random barony deep inside your empire, the county containing that barony will be highlighted); repeat.