Hey RobT, not sure if its the same noise we were hearing but...
Our 2002 Mini Cooper S that we bought second hand had annoying rattles coming from the rear that drove us crazy whenever we drove it around. It was more medium rattle/tapping sound than a heavy clunk though. We checked the rear suspension out but couldn't fault it.
After much trial & error we determined it needed 2 separate repairs to make everything silent again:
1) Replaced the anti-rattle clips in the rear brake calipers (I think the mechanic actually replaced the brake pads with new OEM versions to achieve this). Oddly, it was only the left rear brake pads that were rattling - the right-hand rear pads were fine.
We had a definite improvement once the brake pads were changed.
2) Replaced the bottom part of the boot latch mechanism (wrapping some insulation tape around the tongue of the bootlid latch helped isolate the noise too for a while). Try to shake the bootlid up and down when its closed. If it clunks, either the latch is worn or it needs some adjustment on the bump stops.
After both repairs were done there were no more rattles.
Our 2006 MCS
needed the same bootlid latch repair as well.
Hope this helps & good luck finding your clunk. :-)
Cheers - JJ.