If you don't want the time zone in your output then use:
java.text.SimpleDateFormat dateFormat = new java.text.SimpleDateFormat( "yyyy-MM-dd HH:mm:ss.SSS" )
dateFormat.setTimeZone(wt.util.WTContext.getContext().getTimeZone());
String formattedDate = dateFormat.format(date);
renderAsTimestampPlusTimeZone() includes the time zone so that there is no question or confusion about which time zone is being referenced.
But again if your purpose is logging, then just use log4j and let it do the timestamping of the log lines, allow you to control log verbosity on the fly, etc. Then you only have to worry about formatting dates if you want to log additional timestamps to the log line beyond the time for log line/event itself. While there still is println() based logging in Windchill, there has been an ongoing effort to eradicate it and replace it all with log4j calls. There are loads of advantages to this over directly doing your own file or console output when it comes to logging.