It will all depend on your requirement and the corresponding budget ur willing to extend to.Remember quality and features come at a price.
But some of the common features across different socket types would be :
1. Overall quality of the components used- this would included high quality capacitors, ferrite chokes,quality heatsink if any on VRM section.Heatsinks on north/south bridge depending upon chipset and socket.
2. Features/Upgrade Options:
Capacity of ram supported and no of slots provided- say a mobo offers a max ram of 16gb but has only 2 slots while another has 16Gb support but has 4 slots, the second one woud be preffered for obvious reasons: better upgrade options given that most common ram dese days come in 4Gb modules..so u understand the maths i guess.Then again it depends on how much ram you are willing to install.
Secondly it would extend to other slots like the PCI -E, does the board allow multi video cards to be installed?What is the version of the PCIe slot? Does its support the latest PCIe 3.0 bus standards?
Thirdly ,how many and what types of data drives/optical drives can you install: Some motherboards come with the latest version of SATA (3.0) alongwith the older SATA 2.0,some offer only the older version.Some allow a mix of both SATA and PATA (IDE-in case you still have a perfectly running IDE device you want to continue using)
Then theres support for USB 3.0 version and the number of USB slots its can provide(both USB 3.0/2.0)Does the motherboard provide ample number of headers on motherboard incase you want to use that front panel usb ports and attach another set of usb ports
Not forgetting the usual onboard componets: Hows the embedded sound option? Is its a basic 5.1 ? Does it offer digital otuput? Does the board have multiple Lan ports?Some boards come bundled with their own high grade soundcards that go into your PCi-e slot(not the X16)
Not forgetting overclocking , hows friendly are the options? Does it offer precise control via BIOS? Is the layout good enough to allow installation of most common CPU coolers?Are the VRMS properly cooled etc.
3. Suppport for existing and future cpu's: The VRM of each motherboard allows it to handle a ceratin range of cpus based on their power requirement. For example in AMDs, dual core phenoms are 80W, quads are 95W and quads exceed 125W..some motherboards only allow cpus till 95W, essentially you cant install a more powerful cpu of that generation/socket.
Then again, motherboards will allow upcoming cpus to be installed, like chipsets for sandy bridge allow ivy bridge ....
4. Thoughful layout of componets: This is quite important in micro-atx boards-the most widely available size.Say If the sata slots are too close to the pci-express port you will have issues when you install a double slot /long graphics card. In some cases for budget boards, design is so bad that a long gfx card covers the sata ports and renders them useless! For real!
ATX boards owing to their larger footprint usually have better desgined layout.
5. Warranty:Ranges anywhere between 2-5 years, though most common is the 3 year one.
6. Bundled Goodies : Sometimes makers throw in stuff that simply makes it easy, like the q-connector from asus, which makes the fropntpanel connections easier, RIght angled Sata cables. etc
However there are many points above which cannot be visually verified and a thorough comparsion/review of a product vis-a-vis the other boards will finally aid in in the final choice.
Cheers!!