I wish there was a wiki or something that compared the features of different motherboards, which would make buying motherboards much easier.
The following information about Mini-ITX motherboards was compiled form the various specification pages on the manufacturer’s websites.
Z87 Chipset Motherboards:
| ASRock Z87E-ITX | Asus Maximus VI Impact | Asus Z87I-PRO/Asus Z87I-DELUXE | EVGA Z87 Stinger | Gigabyte GA-Z87N-WIFI | MSI Z87I | |
| Back I/O Ports | ||||||
| PS/2 | 1 | None | None | None | 1 | 1 |
| USB 3.0 | 4 | 4 | 6 | 4 | 4 | 4 |
| USB 2.0 | 2 | 4 | 4 | 2 | 2 | 2 |
| Network | 1 | 1 | 1 | 1 | 2 | 2 |
| eSATA | 1 | 1 | None | 1 | None | None |
| Digital Audio | Optical | Optical | Optical | Optical | Optical | Optical |
| Audio Jacks | 5 | 3 | 3 | 5 | 5 | 6 |
| Video | DisplayPort, HDMI, DVI-I | DisplayPort, HDMI | DisplayPort, HDMI, DVI-I | DisplayPort, HDMI | 2x HDMI, DVI-I | DisplayPort, HDMI, DVI-I |
| Clear CMOS Button | Yes | Yes | Yes | Yes | No | Yes |
| Other | Wi-Fi Antennas | Q-Code LED, DirectKey button, MemOK! button, ROG Connect button | Wi-Fi Antennas, USB BIOS Flashback Button | Bluetooth Transceiver | Wi-Fi Antennas | Wi-Fi Antennas, GO2BIOS |
| Internal I/O | ||||||
| Mini PCIe | 1 (filled) | 1 | None | 1 | 1 (filled) | 1 (filled) |
| USB 3.0 Header | 1 | 1 | 1 | 1 | 1 | 1 |
| USB 2.0 Header | 2 | 1 | 1 | 1 | 1 | 1 |
| SATA 6 Gb/s | 6 | 4 | 6 | 4 | 4 | 4 | Fan Header | 2 | 4 | 4 | 3 | 2 | 2 |
| Other | 1x mSATA/full mini-PCIe | |||||
| LAN Controller | Intel I217 | Intel I217 | Intel I217 | Intel I217 | Intel I217, Atheros AR8161B | 2x Realtek 8111E |
| Audio Codec | Realtek ALC1150 | Realtek ALC1150 | Realtek ALC1150 | Creative Sound Core3D | Realtek ALC892 | Realtek ALC892 |
| Product Page | Link | Link | Z87I-PRO Z87I-DELUXE |
Link | Link | Link |
H87 Chipset Motherboards:
| ASRock H87M-ITX | ASRock H87E-ITX/ac | Asus H87I-PLUS | Gigabyte GA-H87N-WIFI | MSI H87I | ZOTAC H87-ITX WiFi A Series | |
| Back I/O Ports | ||||||
| PS/2 | 1 | 1 | 1 | 1 | 1 | None |
| USB 3.0 | 4 | 4 | 4 | 4 | 4 | 4 |
| USB 2.0 | 2 | 2 | 4 | 2 | 2 | 2 |
| Network | 1 | 1 | 1 | 2 | 1 | 2 |
| eSATA | 1 | 1 | None | None | None | None |
| Digital Audio | Optical | Optical | Optical | Optical | Optical | Optical |
| Audio Jacks | 5 | 5 | 3 | 5 | 6 | 5 |
| Video | HDMI, DVI-D, VGA | DisplayPort, HDMI, DVI-I | HDMI, DVI-D, VGA | 2x HDMI, DVI-I | DisplayPort, HDMI, DVI-I | DisplayPort, HDMI, DVI-I |
| Other | Wi-Fi Antennas | Wi-Fi Antennas | Wi-Fi Antennas, Clear CMOS, GO2BIOS | Wi-Fi Antennas | ||
| Internal I/O | ||||||
| Mini PCIe | None | 1 (filled) | None | 1 (filled) | 1 (filled) | 1 (filled) |
| USB 3.0 Header | 1 | 1 | 1 | 1 | 1 | 1 |
| USB 2.0 Header | 1 | 2 | 2 | 1 | 1 | 2 |
| SATA 6 Gb/s | 4 | 6 | 6 | 4 | 4 | 4 |
| Other | 1x mSATA | |||||
| LAN Controller | Atheros AR8171 | Intel I217 | Intel I217 | Intel I217, Atheros AR8161B | Realtek 8111E | Realtek |
| HD Audio Codec | Realtek ALC892 | Realtek ALC1150 | Realtek ALC887 | Realtek ALC892 | Realtek ALC892 | Realtek | Product Page | Link | Link | Link | Link | Link | Link |
B85 Chipset Motherboards:
| ASRock B85M-ITX | MSI B85I | |
| Back I/O Ports | ||
| PS/2 | 1 | 1 |
| USB 3.0 | 2 | 2 |
| USB 2.0 | 4 | 4 |
| Network | 1 | 1 |
| eSATA | 1 | None |
| Digital Audio | Optical | Optical |
| Audio Jacks | 5 | 3 |
| Video | HDMI, DVI-D, VGA | DisplayPort, HDMI, DVI-I |
| Other | Clear CMOS, GO2BIOS | |
| Internal I/O | ||
| Mini PCIe | None | 1 |
| USB 3.0 Header | 1 | 1 |
| USB 2.0 Header | 1 | 1 |
| SATA 6 Gb/s | 4 | 4 |
| LAN Controller | Atheros AR8171 | Realtek 8111E |
| Audio Codec | Realtek ALC892 | Realtek ALC892 |
| Product Page | Link | Link |
There are also some Thin Mini-ITX motherboards:
H87:
ECS H87H3-TI
Wibtek TH87G-SA
B85:
Wibtek TB85G-SA
Q87 chipset Mini-ITX boards:
ASRock IMB-181-D
ASRock IMB-181-L
BCM MX87QD
Jetway NF9J-Q87
Kontron KTQ87/mITX
MSI MS-98C7
Portwell WADE-8015
H81:
Asus H81I-PLUS
BCM MX81H
DFI HD100-H81
DFI HD101-H81
ECS H81H3-I
MSI MS-98C7
Wibtek TH81G-SA
Knave! I do ambush thee! 
Pingback: Mini-ITX board with eSATA recommendation? - tonymacx86.com
Pingback: Low Profile (half height) GeForce GT 640 card for "ultra" mini-ITX Mac gaming? Approve my kit! - tonymacx86.com
Thank you, exactly what I searched! I thought bout writing a list myself but then I found this! Thank you so much!
Great comparison, helped me a lot. How about adding the new H97 and Z97 models that are now starting to show up in the shops?
I don’t think I have time to compile more comparisons, but perhaps someone can start a wiki?