SQL Developer Data Modeler 3.1 Connection to SQL Server 2008 using Microsoft JDBC Driver

First, download the Microsoft JDBC driver.

Once extracted, I copied the sqljdbc4.jar file into the lib folder under the jdbc folder of the SQL Developer Data Modeler but you just need to know where the jar file is located.
Go to Tools > Preferences > Data Modeler > Third Party JDBC Drivers and click the plus to add the location of the jar file. Then click the OK button.
If on a Windows machine and you want to use integrated security, edit your system path to include the location of the sqljdbc_auth.dll file or copy the sqljdbc_auth.dll to an existing location in your system path, like Windows\System32.
Then click File > Import > Data Dictionary.
Click the Add button.
Click the JDBC tab
Choose Other ThirdParty Driver
For JDBC URL, type jdbc:sqlserver://[serverName[\instanceName][:portNumber]][;property=value[;property=value] – or look here for details about how to form the URL.
For Driver Class, type com.microsoft.sqlserver.jdbc.SQLServerDriver
For Database Type, choose SQL Server.

Assuming your URL is correct, click the test button and you should get success.