The comparison of databases are often required if you are dealing with business applications which has frequent change in databases. Most of the time its the difference between data base stored procedures and table schema.There are so many comparers available which even compares the table data!!.
One method is to write queries to find out sql differences.That suitable if we have some special comparison scenarios.Else use any tool which compares the data.
Here is one free database comparison tool which is free and compares the schema