timeStamp1 = 2011-08-23 14:57:26.662
timeStamp2 = 2011-08-23 14:57:26.9

public static String timeDifference(String now, String prev) {
    try {
        final Date currentParsed = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS").parse(now);
        final Date previousParsed = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS").parse(prev);
        long difference = currentParsed.getTime() - previousParsed.getTime();
        return "" + difference;
    } catch (ParseException e) {
        return "Unknown";
    }
}

final SimpleDateFormat ss_SSS = new SimpleDateFormat("ss.SSS");
ss_SSS.setTimeZone(TimeZone.getTimeZone("GMT"));
for (String text : "0.9, 0.456, 0.123456".split(", ")) {
  System.out.println(text + " parsed as "ss.SSS" is "
      + ss_SSS.parse(text).getTime() + " millis");
}

0.9 parsed as "ss.SSS" is 9 millis
0.456 parsed as "ss.SSS" is 456 millis
0.123456 parsed as "ss.SSS" is 123456 millis

16-JAN-12 04.00.00.999999 PM GMT --> 16 Jan 2012 04:16:39 GMT

16-JAN-12 04.00.00.99999 PM GMT --> 16 Jan 2012 04:01:39 GMT
16-JAN-12 04.00.00.9999 PM GMT --> 16 Jan 2012 04:00:09 GMT
16-JAN-12 04.00.00.999 PM GMT --> 16 Jan 2012 04:00:00 GMT

str = str.replaceAll("(\.[0-9]{3})[0-9]*( [AP]M)", "$1$2");