Mountain Lion firewall is randomly delaying DNS requests
You are right. I diagnose the same rate limiting at the firewall level
on MacOS X 10.7.4 (Lion).

Moreover, if you look at

/usr/bin/sudo tcpdump -i en0 udp port 53


You will notice that the round trip time to get a reply from 8.8.8.8
is much lower then the 40 msec displayed by the server.

On a long test run I had:

;; Query time: 44 msec


and an average roundtrip time of 26 msec:

09:36:14.360564 IP me.53866 &gt; google-public-dns-a.google.com.domain: 9943+ A? www.google.com. (32)
09:36:14.386302 IP google-public-dns-a.google.com.domain &gt; me.53866: 9943 5/0/0 A 173.194.41.180, A 173.194.41.178, A 173.194.41.176, A 173.194.41.177, A 173.194.41.179 (112)


(386302 - 360564 = 26 msec)

To understand this protection mechanism (against basic DOS), look at:

/usr/bin/sudo pfctl -i en0 -s timeouts


The full documentation of this complex command is pfctl(8) Mountain Lion reference manual

Beware this is a powerfull but highly dangerous command. You may easily break your network access (Where is my backup?).