From the documentation of SimpleDateFormat:
Letter Date or Time Component Presentation Examples
S Millisecond Number 978
So it is milliseconds, or 1/1000th of a second. You just format it with on 6 digits, so you add 3 extra leading zeroes...
You can check it this way:
Date d =new Date();
System.out.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.S").format(d));
System.out.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SS").format(d));
System.out.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS").format(d));
System.out.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSSS").format(d));
System.out.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSSSS").format(d));
System.out.println(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSSSSS").format(d));
Output:
2013-10-07 12:13:27.132
2013-10-07 12:13:27.132
2013-10-07 12:13:27.132
2013-10-07 12:13:27.0132
2013-10-07 12:13:27.00132
2013-10-07 12:13:27.000132