It is still reproducible in Ubuntu 12.04.
The "halt -i" command, which should shutdown all the network interfaces doesn't 
seem to work properly.
To workarround, I've added this script to /etc/rc0.d & /etc/rc6.d:

$ cat K99wol_poweroff
#! /bin/bash
# The network interface must be shutdown manually for Wake-on-Lan to work
ifconfig eth0 down

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https://bugs.launchpad.net/bugs/576110

Title:
  WOL not working: eth0 not properly taken down when network-manager is
  stopped

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