I am taking a Cisco QoS Boot Camp course, and the topic of the ECN bits
  arose.

  I'm curious if NetBSD programs (if any) take advantage of ECN.

Last I checked (which was a few months ago, and there has been a
flurry of TCP activity in recent months), NetBSD had support for
handling ECN in tunnel ingress/egress, and altq could do ECN marking
instead of dropping (with RED), but NetBSD's TCP did not support ECN.
Given the recent work, this might be there (in current) now.

Generally ECN is done by a transport protocol, not an application.  So
e.g. ftp data over TCP would take advantage of ECN if both TCP stacks
supported it, with the receiving TCP processing congestion experienced
information from IP headers into the TCP flags to convey to the
sender.

Are you talking about implementing a transport protocol, perhaps over
UDP, in user space?

-- 
        Greg Troxel <gdt@ir.bbn.com>