ConnectionTimeout is the one specified in your connection string and it is the time it takes for a connection.Open() invocation to wait until it gets a connection reference from the connection pool. (Default value is 15 seconds)
CommandTimeout on the other hand is the maximum time for a specific sql command to execute. (Default value is 30 seconds)
If you are doing a bulk insert, etc. you might consider increasing the default commandtimeout. anyone who uses a limit of 0 for any of the two configurations? i believe it is not a good practice for applications to be waiting for life in a deadlock or connection full scenarios.