The error you are providing doesn't really point to a connection that is left open; it is more likely that there is a query that is taking longer than the application expects. You can increase the time it waits for a response, and you could use Sql to find which queries are the most taxing.
If your using C#, the biggest cause of this problem is DataReaders and returning these objects to the upper layers. Most likely some client class is not closing the DataReader it received from your DAL class, leaving the connection open/locked for who knows how long. Track down the DataReaders you're returning and make sure your client classes are closing/disposing of them properly.
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