They're good for second (or third, or fourth) graphics cards, audio interface cards, video capture cards, RAID controllers, SCSI controllers, extra SATA, External SATA... the list goes on and on...
When I get a new mac pro, I plan on buying an extra USB 2 pci express card so I have more ports. Down the road I am sure ill get an eSATA card also and maybe a extra video card for a 3rd monitor. That fills all the slots up right there.
All the newfangled IO that will be out on the market that make your machine look old in the future.
In the old PPC days, this was basically how Apple kept up their old chipsets -- they just added IO to the machine via PCI (and how the currently adds FW to the MacBooks/iMac/Mini/etc.)
Or you can add 3 other video cards, then buy an 8 screen display.