While high end boards have almost no impact on actual performance (I think 3 FPS is being generous), there are still advantages to getting one, including quality, features and reliability.
If you're asking more about how you pick a board, here's my process. Generally, selecting a motherboard is pretty easy.
Once you decide on the CPU, you narrow it down to the socket you need (AMD CPUs use AM3 sockets, i3/i5/i7-8xx CPUs use LGA1156, i7-9xx use LGA1366). This is really the only factor that determines compatibility.
Then you need to decide how many PCI slots you need. If you want to use two video cards (either now or in the future), you need at least two PICe 2.0 16x slots operating at speeds of at least 8x/8x. Generally, more than two PCIe 2.0 slots aren't needed and cost a lot of money.
After that, you need to decide how many other PCI sltos you need for add on cards (sound cards, RAID controllers, whatever). This isn't that important, as most boards have enough slots that you won't use them all.
The last thing to check is that the number of SATA/IDE connnectors is enough to accomadate the number of HDD, opticals, etc. that you have or will have. Most boards have around 5-7 SATA and maybe 1 IDE.
Once you have a list of acceptable boards, it really comes down to quality. Typically, the best brands are Asus and Gigabyte. They're the most reliable and highest quality. After that, many people like MSI, ASRock and EVGA (Intel only, I think). They're slightly lower quality, but are acceptable if you save enough. Any other brand I would eliminate right away.
If you're looking for some good boards, I tend to recommend the same three boards for builds with dual video cards: Gigabyte GA-790XTA-UD4 for AMD, Asus P7P55D-E Pro for i5 and the Gigabyte GA-X58A-UD3R for the i7. For builds that only use a single video card, I tend to recommend: Gigabyte GA-770TA-UD3 for AMD and the Gigabyte GA-P55A-UD3 for i5 (there aren't any single PCIe 2.0 slot board for the i7). I tend to say that anything cheaper than these are low quality and anything more expensive isn't worht the cost.