Frame skipping in most games

So what was the vRAM usage like?
Have you thoroughly scanned the machine for malware/viruses?
Screen resolution ? If 1920x1080/1200 then what level of antialiasing and eye candy are you using? Are you deviating from the default settings determined by the game engines?

When you tried to install the driver;
Did you remove the GTX 580 from the PCI-E x16 slot ? (You probably need to)
Then connect the monitor to the relevent video out on the motherboard (HDMI or DVI-I) and then install the driver (a generic driver should be included in the OS by default in any case) ?
Download from here ?

According to MSI afterburner VRAM usage in Crysis steadily increases from 800 to 1200 and then above(it didn't stop at 1200 by itself, I stopped the game there after half an hour of gameplay). It's a strange thing I don't understand why the used VRAM keeps increasing while the game progresses, you can see the same thing with the Street Cleaner Simulator GPU-z log in post #11, the VRAM used keeps on increasing steadily from 767 MB till 876 MB which is when I quit the game.
I did a virus check, nothing came up.
I play at 1600x900 which is my monitor's max resolution, and I always try to max out the settings if I can (including AA). Default settings for a game are almost always low or medium so I can't leave them unchanged.

Okay I'm going to remove the GPU and see if the onboard graphics work.

OK, I presume the stutter started well before you started getting close to the frame buffer limit. If so, you can safely rule that out.
RAM and vRAM can often climb during gameplay, either through memory leaks, or-especially in RTS/RPG games, where the game map needs to account for an ever increasing number of objects.
Before uninstalling the GTX 580, I'd try playing through a game on reduced image quality and see if that alleviates the issue. Heavy antialiasing, post processing features, PhysX, and hi res textures can take a toll on any card. Maxing the game I.q. levels are generally going to impact framerates on anything above a basic OpenGL or DirectX9 title.

Remember to drop down the game image quality in the game menu before attempting to play using the on-die HD 2000 graphics...they aren't built for performance....any performance.

Tried reducing image quality, it made no difference(actually the stuttering became kind of worse). Anyway lowering graphics settings is for fixing bad framerates, and my framerates are actually very good, just like in the video in post #1.
Okay now I'll remove the graphics card.

Greetings good friend! I am currently using the onboard graphics for the first time ever, and am glad to report that after playing crysis, street cleaner simulator, and portal, that the stuttering is still there and as prominent as ever!
What's the fu%k is he so happy about you're thinking? Well this proves there's nothing wrong with the $600 GPU.
Now what's the next phase? Maybe the CPU? Maybe it's not placed correctly. I am not too trusting of the people who put the PC parts together, since they placed the memory sticks in single channel mode instead of dual channel. So maybe they did something else wrong that is causing the stuttering? Or maybe there's something wrong with the ASUS DVI to D-Sub adaptor, I noticed there are no pins at one end of it.

By the way, I don't see why everyone keeps bashing integrated graphics, they work very well, I can play dota with all settings maxed out, and can play source games at medium settings, and can play crysis at low settings, all of them at 60fps.

Well, on the balance of things I suppose you're ahead. The 580 is still the largest investment in the rig -esp. as it sounded problematical for RMA.
CPU : If the temps are fine, then the only other real option is bent or broken socket pins. Bent can be straightened ( a 0.5mm propelling pencil is the usual tool of choice but you're best bet would be an electronics shop or jeweller if you have no prior experience. Beginners practice is for a giveaway broken board), broken is broken. The CPU can't really be seated incorrectly- it only fits in the socket one way. The cooler can be incorrectly seated, but that generally means a shutdown if bad. You should have noticed temp spikes through the monitoring. You can always dl CoreTemp and monitor in real time which would lead to an easy diagnosis, although if one or two securing pins aren't locked on the Intel cooler it should be very apparent-I.e. movement when there should be none.
Motherboard: Voltage regulation and/or a damaged trace. A degree of specialization required.
PSU : Electronics shop test would be the easiest way to diagnose, as would swapping out for a known good unit
Memory: Run Memtest overnight

Okay completed 5 passes with Memtest, still no errors reported.
I just looked at the CPU it looks fine.
I'm going to start with the cheapest components, by buying some new RAM and see if it works.
What would be a good brand? And would 1600Mhz RAM work for the Intel DH67CL?
Also another question, I bought the PSU randomly, and plugged in whatever cables I saw would fit in, so I have a question, is there a such a thing as a PSU that's incompatible with a motherboard? It's a Thermaltake Toughpower tpx-875M (875 W), the only particular thing I looked for to be compatible is the 8-pin PCI that could fit in my GTX 580.

Just one more question, I don't want to keep piling up the questions but this is another serious problem I have with games, the CPU and GPU usage are often low even though the framerate is far below 60fps. What could be causing this? Example: In fallout 3 I keep geting drops to 40 or 30 fps and when I check GPU usage during this time it's only at 50% and when I check CPU usage it's at 20%. I looked around on other forums, it's a common problem that nobody seems to know the answer to.

Corsair and Kingston are usually pretty much bulletproof on Intel reference boards. Intel's QVL includes most of the major IC manufacturers ( Corsair use Elpida, Hynix, Qimonda, Micron on that list)

See above. The Kingston KHX1600C9D3 kits (4 and 8GB) would be a likely candidate, both from an Intel compatibility and pricing standpoint.

Should be OK. I'm personally not a fan of Tt PSU's, but that's from prior experience and pricing/performance. If the PSU has the requisite connectors and has a rated power excess over the component power draw then it should fit the bill.

No great mystery. Games require a number of components to act in concert. GPU(s) to handle the render, vRAM to hold the textures and other render components, an internal bus to connect the two, CPU for non-GPU computation, CPU physics etc, an external bus (PCI-E) to handle the integration/communication between GPU and CPU, RAM and HDD. The more poorly coded a game is, the greater the number of stalls ( components sitting idle while code is retrieved/computed elsewhere) that appear- lowering framerates and causing inefficiencies (CPU, GPU usage). In addition to poorly coded games, there are instances where the game is coded accurately but the volume of information required induces latency -large game maps, higher levels of detail, longer draw distances, dynamic (or large numbers of) in-game objects, and AI for non playing characters all have the ability to reduce efficiency, as does overburdoning a game engine that originally wasn't designed to support all the features it may at present offer -usually add on's (D3D, lighting effects etc.)

Well I always assumed that either your CPU or GPU would strive to reach its maximum capabilities to get the highest framerate possible. If this low usage is really what's supposed to happen, then what's the point of buying a high end CPU and a high end GPU if the game will only use a fraction of their powers to deliver an unplayable framerate?

They do. Unfortunately it isn't a perfect world

Maybe because the latency, the vagaries of coding, and the limitations of bandwidth, I/O, and storage affect all systems. As for why seek the best CPU and graphics?...well, most people don't- which is why a graphic of the price/point user base resembles a pyramid...and as for what's supposed to happen- that isn't the case. Ideally game (or any) code should run without bottleneck up to the capabilities of the system. I'm simply pointing out why this happens...and making you aware that writing code for a massive number of ever shifting CPU, GPU and storage permutations is somewhat more involved than playing the end product.
Now, rather than further derailing your own troubleshooting thread straight into the realms of metaphysics, maybe we should keep to the topic at hand.

Okay I'll have to wait till monday to get the new RAM.

Hey how you doing? Okay I know I posted just a month too late, I can explain that (maybe later). So you said I should buy Kingston RAM? Okay so would it make a difference if I bought the 1600Mhz RAM? And what amount and number of sticks should I buy?
,I.e.: 2 sticks each 4GB, 4 sticks each 2GB, 4 sticks each 4GB, etc...

Why the question mark? It should be readily apparent from the thread what was said. You talked of buying RAM, I advised buying a set OK'ed by the mobo vendor. Kingston is on the QVL

DDR3-1600 and DDR3-1333 are pretty much the same price. As to any benefit, I'd say yes...but you may feel differently depending upon the workload you use

8GB is usually more than sufficient. 2 x 4GB is a standard module set. It leaves two spare DIMM's if you should ever need an upgrade- unlikely unless you get into content/media creation apps.

Okay then, 2 sticks, 4GB each, 1600Mhz, KINGSTON.
I'll buy them tomorrow probably (don't worry, this time tomorrow doesn't mean next month)

Hmm, maybe on monday. That ****er won't answer the phone.

When you say your drivers are up to date, which drivers have you updated?

Hello again. I was given two KINGSTON 4GB sticks to test them out and see if the RAM is the problem (KVR1333D3N9/4G-SP), it didn't make the slightest difference. All games still frameskip and freeze.

Ok. You've successfully eliminated the graphics card, RAM, hard drive (+ cables), and cooling from the equation. Which leaves you with three of the four variables I listed in post #26.
Before checking these options, I'd say try playing with vsync enabled on the games and see if it makes any difference.

PSU : Easily checked if you have a voltmeter or electrician/electronics service outlet in the vicinity. I wouldn't take it to the same people who built the system. If the rig was put together from the spare parts bin ( no offered warranty on the graphics card is a huge red flag) there could be a conflict of interest thing in play.
Motherboard: Not easily checked, but a faulty motherboard is more likely than a faulty CPU
CPU: No way to tell unless you have a rock-solid known working motherboard to test with - a Catch-22 situation with motherboard or CPU both being unknown quantities.

Okay I could get a voltmeter.
I checked again with him, turns out there is a warranty on every part, my mistake.

Anyways, I never checked the hard drive off the list, just the cables, I mean I didn't replace it with another one. And I'm always playing with vsync on, the measured framerate is always 60fps.