I actually own both the Z10PE-D8 WS and Z10PE-D16 WS, so I can break down the differences for you.
The following assumes that both CPU sockets are used. Do not get either of these boards if you are only going to socket a single CPU.
PCI-E 3.0 x16 slots:
D8 has 7 slots: Odd numbered slots all run at x16 and the even numbered slots run at x8. This allows for 4-way SLI or Crossfire.
D16 has 6 slots: As stated above the first slot can't accommodate most full sized GPUs due to the position of the CPU socket behind it. However, ASUS took this into account and so slots 1 and 3 run at x8, while slots 2, 4, 5 and 6 run at x16. This allows for 3-way SLI or Crossfire while leaving the x8 slot 1 available for any card that doesn't extend too far beyond the slot's latch.
(Theoretically, the D16 could support 4-way SLI if you had single-slot width GPUs.)
USB:
D8: 6 USB 3.0 ports on the rear panel and two headers on the board that offer 2 additional ports each for a total of 10 USB 3.0 ports.
2 USB 2.0 ports on the rear panel and two headers on the board that offer 2 additional ports each for a total of 6 USB 2.0 ports.
D16: 4 USB 3.0 ports on the rear panel and only a single header on the board that offers 2 additional ports for a total of 6 USB 3.0 ports.
4 USB 2.0 ports on the rear panel and only a single header on the board that offers 2 additional ports for a total of 6 USB 2.0 ports.
Storage:
D8: 4 SATA 6Gb/s plus 4 SSATA 6Gb/s ports plus two additional pairs of SATA 6Gb/s ports that can either be used as 4 standard ports or as 2 10GB/s ports that offer the same old standard SATA devices a higher transfer rate. The M.2 slot is 32Gb/s PCI-E Gen3 x4.
D16: 6 SATA 6Gb/s plus 4 SSATA 6Gb/s ports. The M.2 slot is 10Gb/s PCI-E Gen2 x2 and shares bandwidth with SSATA port 4.
Memory:
D8: 8 slots. 512GB max.
D16: 16 slots. 1024GB max.
Both boards support RDIMMs (ECC ram) only.
CPU: (I mention this only because it's how I ended up with both boards.)
D8: Xeon E5-2689 v4 is not on the list of supported CPUs for this board. It works with only one socketed, but it will not run this model in both sockets. (I think it's due to the E5-2689 v4 consuming 165W each.)
D16: Xeon E5-2689 v4 is on the list of supported CPUs for this board and functions with them in both sockets.
BMC:
D8: There is a header on the board to allow for the addition of a separately purchased ASMB8-iKVM chip to allow for remote management features.
D16: ASMB8-iKVM is integrated with the board, and offers a third RJ45 (ethernet) port on the back panel dedicated to its remote management functions.