The most important thing you need to know is what kind of PC you are building. Is this for gaming? Is this for photo editing? Is this for email and internet? If you are not sure exactly, you might find this article helpful: Best Desktop Computer Buying Guides and Building Tips.
Once you know the type of PC you want, you know how high end a motherboard you need. Probably the most important question is whether you want this PC for heavy duty gaming. If you do, that raises some additional questions you need to decide on before making a selection.
The biggest one is whether or not you want to do SLI or Crossfire. In short, those are technologies that allow you to use two graphics card simultaneously for enhanced gaming performance. SLI is for NVIDIA graphics cards, and Crossfire is for ATI graphics cards. The gains from this are minimal on a per dollar and per watt basis and many games still have little or no SLI/Crossfire support. Going SLI/Crossfire means you need a more expensive motherboard, two graphics cards, a more expensive power supply, and possibly more fans/cooling. On the plus side, SLI/Crossfire can give you better performance now, or a path to upgrade later if you buy one high end graphics card now, and buy the second, matching one later when prices fall.
There are a few hardware specifications that are absolutely vital when you shop for a motherboard.
CPU Socket Type: This is the type of CPU the motherboard supports. You will probably choose your CPU before your motherboard, so make sure these match.
CPU Type: This is also important in making sure your CPU is compatible. Most likely, if the socket type is compatible this will be compatible as well. But double check!
Number of Memory Slots: This is usually 2 or 4. This is the number of RAM chips you can install. 
Number of Pins: This is the number of pins supported in the RAM slots. If you buy the wrong RAM, it will not fit in the motherboard.
Memory Standard: This is just as important as the number of pins. An example of a memory standard is "DDR2". You need to buy RAM that matches this.
Expansion Slots: Pay especially close attention to the number of PCI Express 2.0 x16 slots (most high end graphics cards require at least a PCI Express 1.0 x16), regular or x1 PCI Express Slots, and plain PCI Slots. You need to make sure you have enough of the right types of slots for any cards you plan to add: graphics cards, sound cards, video capture cards, etc. Differences between PCI, PCI-E and x16 lanes slots are explained here.
Storage Devices: At the time of this article, you will most likely buy a SATA hard drive. So make sure your motherboard supports SATA storage devices.
Physical Spec: Most desktop builders are looking for ATX form factor, available in three sizes; Extended, normal, and Micro. You can put a smaller ATX board in a larger ATX case (e.g.: Micro board in normal case or normal board in E-ATX), but obviously not the opposite. If you have a specific case in mind that is not ATX, make sure it matches with the physical spec for this motherboard.