I just built a brand new machine the other day. Everything was going really great until I was about an hour into playing CoD4 when my machine shut off. Immediately I figured it was a heat problem. Low and behold the cpu was overheating because I didn't seat the stock cooler properly. So I checked it and decided that the thermal paste that came on it wasn't good, so I removed it and applied some arctic silver.
 
It runs fine now, but I got speedfan anyways and I'm pretty sure I'm running far too hot. What do you think? (System is Q6600 with stock cooler on EVGA 780i, in a NZXT Tempest case)
 

If that's idle temperature, then yes, it's too hot. Run prime95 while monitoring temperature. Stress at least an hour.
http://files.extremeoverclocking.com/file.php?f=103

Agreed, if that's an idle temp, then its way too hot. For a comparison temp, I have an overclocked QX9650, and at present am running F@H, a game, and two apps, and my CPU temp is 27c. Core zero, presently the hottest, is all of 47c, with the others running between 37c and 41c. First things first, get rid of your stock cooler and get a better one. Among the less expensive coolers, the Arctic Freezer 7 Pro is reported as a good one, as well as the Xigmatek Rifle.

I'm running 64 bit vista actually.
 
Anyways just started the stress and I'm at
 
Pretty sure that's not good whatsoever, so I guess I need to look at trying the damn thermal paste application all over again.
 
Edit: Yeah I plan on getting a different cooler, but even still I shouldn't be running this hot at stock. I'm not going to get a new cooler for a couple weeks so I need this thing to run fine at stock first before I move on to something else.

It's not the thermal paste, but the cooler. You need a new one.

Aftermarket cooler or not, correct me if I'm wrong but this shouldn't be running this hot at stock?

Oh lord. Your CPU is at 87c which is way above the thermal limit (max temp) on that Q6600. I think Intel reports the Thermal Limit at 72c.
 
Definitely need a new cooler. The Q6600's tend to run pretty warm, and everyone recommends replacing the stock cooler.
 
I have a cheap $35 Maxcool something or another I got on TigerDirect. And at stock speeds (2.4Ghz) I idle in the 30's, and top out in games at like 48c?
 
Your temps being well over 80c I wouldn't do anything with your system other than web browsing to buy a cooler until the new one arrives.

 
I guess that depends on how much airflow you have through your case. The stock coolers for the Q6600 are generally not consider by most people on Tom's to be sufficient.
 
Looking at your case online, it looks like you've got decent air flow (potentially). 2 front intakes, 1 rear exhaust, 2 top exhaust, and a side intake. All of them are 120mm or larger. So you should have good flowthrough so long as your cables and such don't cause a severe restriction.
 
If you're still running this hot, with all of those fans running, that stock cooler is either extremely underpowered for that processor, or it still isn't seated properly. Running 80c+ at 100% usage  at stock speeds is ridiculously hot.

Guess I'll try yet another reseat.
 
As far as after market coolers go, I've been looking at the Tuniq Tower and the TRUE... my only real reservation about either is they're freaking gigantic and somehow I think they're going to look absolutely hideous in my case. Any opinions on aesthetics? I obviously wouldn't sacrifice performance for beauty, but if I had the option of a cooler that performed as well as the Tuniq or the TRUE and looked better I'd go with it.

I'm not as big on the "looks" of my PC tower. Then again, my tower sits on the floor beside my desk where I can't see it. So having a clear side on my case and such really means nothing to me.
 
Aesthetics (beauty) is truly in the eye of the beholder. Personally, I just pick whatever performs the best for the money I have to spend. Computers for me are about performance & picture on screen. I could care less what the box on the floor looks like.
 
If you try to reseat that cooler again, make sure you clean off the heatsink so you don't have any of that old thermal paste crud on there.
 
Still though, get an aftermarket cooler. Really no argument against it.

Definitely go for an aftermarket - as for something that looks different, the Zalmans are pretty good, and look different (it's personal preference over whether it's better).

For reference, this is what I use for q6600@3.6ghz.
http://www.newegg.com/Product/Prod [...] 6835887011
Full load temperature on prime95 tops at 58C.

 
If I remember correctly, your CPU shouldn't be running higher than 65c, much less 87c. I would suggest not stressing it at all until you can get a better cooler on it. The stock Intel coolers are none too good, but 87c is ridiculous. I'm surprised that there wasn't an automatic shot down triggered. As for the Tunic and the TRUE, those are large coolers, but they should fit the case as long as there is no side fan in the way. Keep in mind that you have to buy a separate fan for a TRUE. I use a TRUE combined with a Noctua fan and it works very well.  
 
As jerreece said, if you reseat your present cooler, make sure all the old paste is cleaned off before you apply new stuff. You might also check the heatsink and make sure its surface is level. If it isn't, a bit of lapping might be in order.  

Im wondering if it is reading it properly? If I recall, at 85C the processor shuts down.

Isn't auto shutdown triggered by motherboard? I heard that some allow you to turn it off in bios. In any case, thermal threshold is 71C, and it will throttle multiplier back to 6x if over that limit.

Get Coretemp.  What your using, unless calibrated is usually wrong.  My speedfan reads it wrong.  It's the way it pulls the info.  Coretemp is able to extract the actual temp, don't ask me how but it's the gold standard to post temps while benchmarking.

It over-reports temp. But more pros err on the side of caution, and think overreporting as more desireable than underreporting. The other ones underreports.

As for "calibration," it's more like an educated guess. There is no real way to pin down actual exact temperature based on those sensors.

I would use realtemp and calibrate it.