Since you are referring to Hyper Transport it looks as though you are going to use AMD CPU? If so use the Socket AM3. Now comes down to Series: Athlon II or Phenom II and then number of cores; single, dual, triple, quad, or six core? This comes down to two things: Preference (cpu speed) and price. The CPU you choose could in some cases affect the motherboard use use. If you stick with AM3 then choose an AMD mobo with socket AM3. This will make choosing your mobo easier. The mobo also comes down to preference and price. Some mobos are higher-end some mid-range and otheres are low-end. If price isnt and issue and you want a good gaming ring I would stick the better name brands; EVGA, ASUS, Gigabyte and a couple more. Since you are building a gaming rig the mobo you choose in some cases will depend on the graphics card. Do you want Nvidia or AMD GPU? Do you want to do Nvidia SLI or AMD Crossfire? This could depend on the mobo as some mobos may not allow SLI and Crossfire. If only using single Graphics then most likely you shouldn't run into issues but keep that in mind should you choose to add a second graphics card later. When you choose the mobo look at the FSB speeds. that will depend on the memory you choose. there are many options for memory. Memory is very sensitive, don't be cheap here. Cheap memory can cause problems. Good memory: GSkill, Corsair, Kingston HyperX, Patriot. If you Choose AM3 mobo you will be using 240-pin DDR3. The memory speed (PC3 XXXXX) doesn't have to be an exact match on the mobo memory speed. As long as it's in range it will work. It just means if your mobo memory speed is compatible with PC3 12800 and you buy memory that is PC3 10666 the the max memory speed will be PC3 10666. The only way you will notice a differnce is when you benchmark otherwise you wont see a big diff between the two, for example.
I did the above writeup on the fly. I might have left something out. Let me know if you have any more questions.