See the testcase at https://bugzilla.mozilla.org/attachment.cgi?id=523831 on which the yellow square should be on top of the red one. In particular, the 2d transforms specification says that transformed elements act like position:relative for stacking purposes, so z-index should apply to them.
It's not obvious to me that z-index should apply. They act as positioning containers, but that doesn't necessarily mean that z-index applies. This is worth a post on www-style.
http://lists.w3.org/Archives/Public/www-style/2011Apr/0648.html
Consensus was to not have z-index apply.