First of all, here are my specs:

Intel C2D E6600
2GB PC2-6400
ATI X1900XT
535W ENERMAX
All at stock speeds

Now, the problem I have is that my CPU is running extremely hot and I have no idea why this is happening. I have checked the temperature of it with many programs, including Core Temp, SiSoftware Sandra, RightMark CPU Clock and TAT, and they are all showing that the temperature is around 75-80. I have looked around in my case and the airflow is fine and is fitted with 2 120mm fans and 1 90mm fan with the stock heatsink. The air is cool inside but when I touch the heatsink, it is boiling hot and I have no idea why. Can someone help me out with what I can do to resolve this problem, perhaps get new 120+90mm fans and heatsinks, if so, any reccomendations? Thermal paste? I really don't know..

My knee-jerk reaction is that your HS is not mounted properly, or if it was, it has come loose.

Is this a new build? If so, reseat your HS. Take the mobo out if thats what it takes to do it properly. If it was running cool then lately has goten hot I would definatly say the HS came loose in a move of the case or something. Have you taken or moved the case lately?

I mean really the only think that makes your temperature too hot is poor cooling. Case ventilation is not going to drop you 20C which is where you really want to be. So you need to examine the HS mounting very carefully.

It's not really a new build (around a year old I guess) and now is really the only time I started monitoring temps and stuff as I was wanting to do some overclocking. I have already checked that the heatsink is mounted properly and it seems that it is on securely.

Ohh wait one more thing. Are you running ALL those programs at once or are you checking then shutting down each program individually. I have read about problems arising when running several temp monitoring programs at once.

Also try one more program. run SpeedFan (by itself) and what does it read. You also didnt mention if these were "load temps I assume".

You say its stock, so it not a matter of high voltage or OC. That basically narrows it down to roughly 3 possibilities:
Improper cooling

Improper software readouts: TAT and coretemp WILL read 15C too high on my E4300

bad thermal diodes

well bad diodes is not really an option since ther is NO WAY for software to directly access the CPU's thermal diode. The CPU doesnt have the capability. period. Also the fact that your "touch" of the HS tends to indicate that the HS is hotter then hell, and so therefore the software readouts (approximate guesses) are roughly correct.

So is the HS's fan operating? Are the fan or HS fins dirty? If not, I HIGHLY recommend removing, cleaning, reapplying thermal paste, and remounting the HS.

If its a matter of software, ie TAT or coretemp reading 15C too high then -15C would put you at about 65C which ....ehhhhen might not be unreasonably high for loads with stock cooling. 65C is a bit warm. Check BIOS to "BE SURE" your core voltage is at 1.325 or whatever stock V. is on a E6600.

No, I'm running them all seperately, closing, then running a different one. I've tried speedfan and it comes up with the same temperatures again. These temperatures are just normal temperatures when I have nothing running.

Yeah, the HS fan is operating fine and the fins look fine but I guess I will give it a quick clean and find some thermal paste to re-apply. What should I use to clean the HS? Also, is the CPU recieving damage thanks to this immense heat or is it fine?

clean it with some isopropyl alcohol. Use a 90% minimum if you can.

Your CPU will throttle back before it damages itself but the high temps certainly cannot be good. It does have an internal "shut down" threshhold temp to prevent temp burnout. 70+C idle temp can only be cause by improper heatsink somethingl.

Do you have a digital camera? Pull the HS and take a picture of both the CPU and HS bottom.

Its got to be a bad contact between the CPU and the HS. Either from bad or non-existant thermal paste, extreme concave of either or both CPU or HS, or in all likelyhood one or more of the plastic mounting pins is compromised.

Its gotta be a bad mount. There really isnt anything else that I have ever heard of that causes extreme temps.

you clean the dust? u need to post more specs - your voltage must be high? or amps high?

3 thinkgs no cooling, too high volts or too high amps - possible rouge programs making your cpu run all day

any new programs reinstall or try a roll back to pre problem

I took out the heatsink and it had a lot of dust inside it, so I took out much of the dust and put it back in, however I didn't have any thermal paste to put on. I've run some of the programs and they are now at 85/83 for CPU0/CPU1. What the hell?
How would I go about posting the specs for voltages / amps?

If it's a problem with the heatsink, can't I just get a new one to replace the stock one and then clean the CPU, re-apply thermal paste and put on the new heatsink? I was reccommended the Thermalright Ultra-120 heatsink, do you have to take the motherboard out to put this heatsink in? I was also thinking of getting a couple of Zalman ZM-F3 120mm fans to replace my stock fans which are kinda crappy. This would surely sort my problem?
I just checked RightMark CPU Clock and it's saying CPU core overheat detected - 99%....

Turn off your computer right away and do not turn it on again until you get some thermal paste! You could ruin your processor by running it without thermal paste. Clean heatsink fins with a vaccum cleaner or air compressor and clean the base and the heat spreader on your cpu with 90% alcohol. Apply your new thermal paste according to the instructions included with it. Make sure that the pins on the heatsink are properly engaged to the motherboard. They can be a pain in the butt to get them locked down properly.

I have just ordered a new heatsink, the Thermalright Ultra-120 with a couple of new case fans, some thermal compound and a CPU/heatsink cleaner to get rid of the current thermal compound on the CPU. Am I correct in thinking that I should first remove the stock heatsink, then clean the thermal compound on the CPU (how am I meant to do this correctly? remove the CPU from the bit it's in then clean it softly? how would I dry it?) After this I put some fresh new thermal compound on the CPU and place the new heatsink on? If someone could confirm this order to do it in for me, I'd greatly appreciate it. Thanks!

Just take a soft cloth and dampen it with the alcohol or cpu cleaner that you ordered and wipe off the top of the cpu. Do that a couple of times until the cpu is cleaned.The cleaner will evaporate on its own. You do not have to dry it. You do not have to remove the cpu from the motherboard to clean it! Other than that it looks like you pretty much have the proper order for replacing the heatsink. That Thermaright heatsink is awesome from the reviews I read (go to Frostytech website for review) your temps should drop by at least 50% if not more!

just gonna toss in my 2 cents here. make sure there is no fan control on.
since most boards do not read from the core, they read from the socket(LGA in this case) they read much cooler. then fan controls keep the fan slow and let it warm up.

Hell my quad fan wont even spin up until the system get going(i am gonna fix this, but the temps where stupid low then, like 27-30c cause the room was 18c and speedstep is on).

You need to list your BIOS settting in regards to your CPU settings ie. FSB, CPU multiplier, core voltage. You say stock but have yet to list what "stock" is on your board. We need to know this information before any definative answers can be given. But I still think its a mounting problem with your HS. I mean everyone "thinks" they mounted it correctly, but there are thousands of threads just like this from people who in fact did not mount the HS correctly. Hell Im a rock solid 6'4" 225 and I had a hellofa time snapping the plastic push pins on my ninja down. I thought for sure I was going to break them or the board for sure.