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I'm on 12.10, and have always used dnsmasq. A few days ago I noticed strange messages during boot:

NetworkManager[1316]: <warn> DNS: plugin dnsmasq update failed
dnsmasq[1302]: failed to create listening socket for Address already in use
dnsmasq[1302]: FAILED to start up
NetworkManager[1316]: <info> DNS: starting dnsmasq...
NetworkManager[1316]: <error> [1362028900.869958] [nm-dns-dnsmasq.c:390] update(): dnsmasq not available on the bus, can't update servers.
NetworkManager[1316]: <error> [1362028900.869979] [nm-dns-dnsmasq.c:392] update(): dnsmasq owner not found on bus: Could not get owner of name 'org.freedesktop.NetworkManager.dnsmasq': no such name
NetworkManager[1316]: <warn> DNS: plugin dnsmasq update failed
dnsmasq[1876]: warning: no upstream servers configured

Here is my /etc/dnsmasq.conf:

Here is my /etc/dnsmasq.d/network-manager:

# Tell any system-wide dnsmasq instance to make sure to bind to interfaces
# instead of listening on
# WARNING: changes to this file will get lost if network-manager is removed.

If further information is needed, please ask!

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up vote 9 down vote accepted

Extracted from link

Note that the package "dnsmasq" interferes with Network Manager which can use "dnsmasq-base" to provide DHCP services when sharing an internet connection. Therefore, if you use network manager (fine in simple set-ups only), then install dnsmasq-base, but not dnsmasq. If you have a more complicated set-up, uninstall network manager, use dnsmasq, or similar software (bind9, dhcpd, etc), and configure things by hand.

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