OK, getting it working in mythbuntu was easy – I just selected the appropriate remote from the control centre. But that’s only half of it. The lirc config files are to be found in ~/.lirc/. So for now, here’s my mythtv config file for a MCE version 1 remote.
And now here’s my mplayer one:
Update: so it turns out there’s a problem using a MCE remote for your mythbox when you also have a XBOX360, certain buttons turn the xbox on, d’oh! So I taped a bit of tinfoil over the IR reciever on my xbox.