How do I find merged Records?

In the immediate aftermath (and a short time thereafter), you can find deleted records with a MasterRecordId in the Recycle Bin.

SELECT MasterRecordId FROM Account
WHERE MasterRecordId != null
ALL ROWS

You might be able to use a left inner join but I am unable to confirm currently.

SELECT Id FROM Account WHERE Id IN (/*above query*/)

Here's the description of the field from the SOAP API documentation:

If this object was deleted as the result of a merge, this field contains the ID of the record that was kept. If this object was deleted for any other reason or has not been deleted, the value is null.

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In terms of how to make use of this field, it should be populated in an after delete context. Implementing a trigger handler pattern and error handling are recommended, but omitted here for brevity:

trigger Account on Account (after delete)
{
    if (trigger.isAfter)
    {
        if (trigger.isDelete)
        {
            Map<Id, Account> masterRecords = new Map<Id, Account>();
            for (Account record : trigger.old)
            {
                masterRecords.put(
                    record.MasterRecordId,
                    new Account(Id=record.MasterRecordId, Is_Merged__c=true)
                );
            }
            update masterRecords.values();
        }
    }
}

If you are using AccountHistory, then very easy to do from AccountHistory table with out worrying about recycle bin.

SELECT AccountId where Field = 'accountMerged'