John Doe Jr.
Note that there are no commas. Also note that there are no hard and fast rules for the use of Jr. In some cases where the first and last name are the same and the middle name is different, the use of Jr is still used. Usually though, in order to be able to use Jr in the name, the entire name should be identical to the fathers name.
Check out Suffix (name - Wikipedia, the free encyclopedia) for more information on the use of Jr.
Hope this helps.