I would find someone who has built a PC from scratch before or start doing a lot of research. Anyone can buy components but it takes patience and skill to make it all work as I'm sure some here would agree. Someone's experience could be a great help and save you some wasted cash. The first thing to consider is how much you want to spend then people can suggest components. I know I could spend a few thousand (if I had it to spend )
There are some good videos on Youtube of people building PCs to show others how to do it.
Do not scrimp on the PSU. It is the heart of your system, and a bad one can cause all kinds of problems, from instability to frying other parts when it dies.
A quality modern PSU has full range active PFC (no little voltage switch) and some level of 80+ certification for efficiency. Seasonic, Antec, Corsair, XFX, and Enermax/LEPA are among the better brands. Read some PSU reviews at www.hardwaresecrets.com, www.jonnyguru.com, and/or www.hardocp.com to get an idea of the differences between a good one and a bad one.
You need to know what you're dealing with here. You don't just buy a cpu, memory, GPU and slap it in any mobo. You need to know certain factors like differences between AMD and Intel; CPU Socket types, Memory clock speeds and Memory types (DDR'X'). You need to understand mobo's and what and what won't work with what piece of hardware. You need to make sure you powersupply is beefy enough to power all your harware and that depends on what hardware you buy.
Since you are new I strongly suggest you research BEFORE you purchase anything otherwise you will be doing a lot of RMA's. Newegg is a great place to buy computer parts AND it also has useful reviews on all hardware.
I don't want to scare you off b/c building your own rig is fun and rewarding.
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.
If you want to use Intel CPU the clock speeds, sockets and FSB will be completely different. There is nothing wrong with using either. I prefer AMD but thats just me.
If you are in no hurry to buy this I might suggest waiting for AMD to release it new AMD 'Bulldozer' CPU. It was supposed to be release this month BUT not sure what the status is. Keep in mind though it might be a bit priceier since its new.
BTW, on the memory, I would buy no less than 4GB. 6-8 is even better. Also, some mobos come with onboard graphics. I'm a gamer and I would NEVER rely on any onboard GPU. Onboard GPU's are for typical computing use. Most onboard GPU's will not push games, espeically high-end games. In-fact I make sure my mobo's don't have an onboard GPU if i'm using it for gaming. I only use true graphics 'cards'.
I did leave something out...you asked about thermal paste. Its true most (if not all) heatsinks or cpu/heatsinks comes with either a pad already on the heatsink or a tube of thermal grease/paste. But if you want the best then Arctic Silver 5 is the best. You only need a small tube. Search the net for instructions on how to properly apply it. If you buy AS5 and the heatsink already has a pad you can carefully remove it buy using rubbing alochol or something. I may have even used paint thinner before.
Last ichecked you DO NOT need 2 same video cards if running AMD Crossfire (google it and double check me). You DO, however, need SAME 2 video cards if running nvidia SLI. I have run nvidia SLI so this i'm sure of unless they recently changed it.
From what I understand the AMD Bulldozer is supposed to something great. BUT, there has been little info on the specs and no real tests or benchmark released that i'm aware of. I might suggest a google search and see what might be posted. AMD's phenom II tends to take a back seat to intel's i7 highend series but they are usually more expensive. The only exception might be AMD phenom 2 x6. That said, if you're looking for AMD look at the phenom 2 x6 series. They actually come very close (and in some cases may surpass) Intel's i7 series. There is speculation the AMD Bulldozer might actually clobber Intesl's i7 series. By now you might have guessed i'm a bit biased towards AMD. We need AMD to stay alove to keep CPU prices down somewhat. I might suggest you google AMD phenom 2 x6 vs Intel i7 and see what others are saying. Keep in mind you can overclock any of these but since you are new I would strongly suggest you wait a while before doing so. First get the system built and make sure all is stable. Overclocking IS NOT REQUIRED! its only a way to get more horsepower if you want it.