While the processor, graphics card, and even the RAM speak directly to questions around performance, the motherboard will answer the more fundamental question of what you can run on your PC. Hardware compatibility centers around the motherboard, because it is the body of a PC, into which all other parts must fit.
As recently as ten years ago, demanding software (whether business titles or games) often needed all components to meet very specific minimum requirements in order to run properly. You chose those parts, then tried to find a motherboard that was compatible with all of them. That's rare today. Pick a program, any program, and regardless of what the benchmarks say, almost any motherboard will accept parts fast enough or big enough to run that software well.
Motherboard selection priorities can be summed up in four expressions, two of them related: size, cost, longevity and future-resistance. The cheapest Intel H81 or AMD 760G board, outfitted with the appropriate CPU, graphics card and memory can make any game that needs a single graphics card functionally as enjoyable as a top-dollar Intel Z170 or AMD 990FX motherboard, even though there will certainly be a few frames per second performance difference between them.
The big difference will be what happens in two or three years. If you want a second graphics card, the H81 and 760G boards won't help, and if overclocking the CPU becomes essential, the H81 will say “Overclocking? What’s that?” and the 760G may simply die trying. If you can anticipate your future needs as well as your current requirements, you can select the right motherboard. Check out the number and type of expansion slots. How many USB ports are available? Is the onboard sound good enough, and if not, is there a place to add a decent sound card? Can I plug in all my drives? Can I make the CPU run faster than factory specifications? Safely?
Some of these questions can be answered just by looking at the size of the board.
Every PC ever built goes somewhere. Maybe it’s on the floor or on top of a big desk, but it might be in a rack, on a shelf, share a [small] desk with other accoutrements of a typical office worker, or be placed somewhere that puts practical limits on size.
Here are the most common form factors. As you can see, each of them has a different number of expansion slots, into which cards such as display adapters, wireless NICs, and tuner cards can be inserted. The EATX form factor is deeper than ATX, but adds no additional slots. If you know you need a graphics card, professional-quality sound card, and plan to re-use a wireless NIC, then Mini-ITX and DTX are not for you. If it needs to fit in an alcove of a desk, then ATX (or EATX) may not be viable options.
Let’s take a look at a typical higher level motherboard for an example of connector and port types.
Here we see some common port and connector types. Of course, not all boards feature all types, and some components may be located differently. Just as some PCIe slots may be wired for fewer lanes than the slot length suggests (or have some lanes disabled depending on what other slots are in use), the M.2 connector at (6) in the diagram above may have up to four PCIe 3.0 or 2.0 lanes in it, or it may have one or two SATA ports in it, or a combination of these interfaces.
Here, we see some PCIe slots. Top to bottom, they (and their most common usages) are X16 (for graphics cards), X8 (also for graphics cards when more than one is used), and X4 (RAID cards, PCIe SSDs). In addition, even shorter X1 slots are more commonly available, for wireless NICs and port expansion, including USB, SATA, and legacy port types.
In the example above, notice that the forward (right) end of the smaller slots are not enclosed. Most PCIe cards should work in open-ended slots with fewer PCIe lanes than the cards possess, but the performance penalty may be severe. Also, on all but the most advanced chipsets, only the primary PCIe x16 nearest the CPU will electrically possess all 16 pathways. Secondary and tertiary slots may be wired as x8 or x4. Nvidia will not allow an X4 slot to be used for a second graphics card in SLI, and Crossfire performance of multiple AMD graphics cards may take a performance hit, especially if the slots are the older PCIe 2.0 instead of the current 3.0. Some boards offer one or more legacy PCI slots, which are similar in length to PCIe X16 slots, but set closer to the rear edge, and won’t have retention clips at their forward edges.