ntpd: consistently incorrect time on mid-2013 MacBook Air
The server keyword of ntp.conf(5) would appear to configure only a single server, even if the provided hostname resolves to more than one IP address.

It would appear that the specific server that was being selected is a PoS.

mba: {4899} ntpdc -s ; ntpdc -sn
     remote           local      st poll reach  delay   offset    disp
=======================================================================
*time.apple.com  129.xx.xxx.xxx   2 4096  377 0.07106  0.000248 0.24763
     remote           local      st poll reach  delay   offset    disp
=======================================================================
*17.151.16.22    129.xx.xxx.xxx   2 4096  377 0.07106  0.000248 0.24763
mba: {4900} ntpdate -d 17.151.16.22 |&amp; tail -1 ; \
?           ntpdate -d time.apple.com |&amp; tail -1 ; \
?           ntpdate -d ntp1.yycix.ca |&amp; tail -1
26 Nov 01:49:13 ntpdate[97738]: adjust time server 17.151.16.22 offset -0.000318 sec
26 Nov 01:49:16 ntpdate[97740]: adjust time server 17.171.4.15 offset -0.006493 sec
26 Nov 01:49:16 ntpdate[97742]: adjust time server 192.75.191.6 offset -0.006443 sec
mba: {4901}


Going to Date &amp; Time Preferences, and providing a comma-separated list of valid NTP servers seems to fix the issue.

Providing a comma-separated list in GUI results in several server entries in /etc/ntp.conf, although you have to make sure that the hostnames themselves are different (otherwise, the repeated hostnames don't result in any extra actual servers being selected, as per ntpq -p).

mba: {5104} cat /etc/ntp.conf
server ntp1.yycix.ca
server time.nist.gov
server tick.usask.ca
server tock.usask.ca
server clock.nyc.he.net
mba: {5105} ntpq -p
     remote           refid      st t when poll reach   delay   offset  jitter
==============================================================================
+ntp1.yycix.ca   .GPS.            1 u  138  512  377   56.517   -0.662   0.319
-2610:20:6f15:15 .ACTS.           1 u  117  512  377   27.975   -1.774   0.989
+tick.usask.ca   .GPS.            1 u  456  512  377   31.388   -0.636   0.135
*tock.usask.ca   .GPS.            1 u  124  512  377   31.486   -0.864   0.413
-clock.nyc.he.ne .CDMA.           1 u  139  512  377   26.860   -2.161   0.194
mba: {5106}


A list of servers is available at http://support.ntp.org/servers; you have to try to select the servers that are close to you, especially not just geographically, but network-wise.