On my new '06 4.8, there is actually a carpeted tray underneath the cargo floor panel. That is, there is a floor panel w/the rubber tie-downs, and then under that if you lift up the floor, you will find a hard spare tire cover/tray that is carpeted. Although it is only 3" deep or so, you can store some tools, jumper cables, etc. on it easily. The tray itself is held in place by a couple of clips that you turn to remove. Under all that is the mini-sized spare that comes with the 20" wheels on the 4.8 instead of a full size spare. I don't see why you couldn't use the same parts on a 3.0 or 4.4, but it would probably require use of the mini-spare from the looks of it.

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'06 X5 4.8is, TiAg/black, cold weather pkg., comfort seats
'07 750Li, TiAg/black, sport pkg.
'05 Ford F350 silver met./slate gray, Lariat, 6.0 PSD, CC, DRW, FX4