Don't get me wrong, the X2 6000+ is still a great processor, it's just that why would you get that when you could get a better performing processor for about the same price?
And, to answer your question about a 2.66 GHz (E6750) processor being faster than a 3.0 GHz (X2 64 6000+) processor, it happens. It depends on the frequency of the front side bus (fsb) and the bus/core ratio. The front side bus is what exchanges the data between the processor and the video card and RAM (collectively known as the northbridge). So you can have the fastest processor in the world that will analyze and process a lot of information very quickly received from the fsb, but if the fsb is slow getting the information there in the first place, it negates the purpose of having a fast processor.
So, since the AMD 64 X2 6000+ has a FSB with a speed of 800MHz and the Intel E6750 has a FSB with a speed of 1333 MHz, the information traveling from the video card(s) and/or RAM will get to the cpu almost 1.7 times faster in the E6750 than it will in the X2 6000+.
Think of the both of the processors' FSBs as highways for information. The E6750's FSB would be (roughly) an eight-lane highway while the 6000+'s FSB would only be a five-lane highway.
I'm not that great at explaining things so I hope you understood that.
Oh, and you want to be looking at the Intel Core 2 Duo processor line (specifically the E6750), not the Quad Cores that will cost you an arm and a leg. Quad Cores are only worth buying if you do a lot of video editing/encoding/recording or you want this computer to last another 5-6+ years (as a lot of next-gen games will be made specifically to take advantage of quad core features). Since pc games are always in the neighborhood of two years behind the hardware upgrades due to their development time, very few games are available today that are designed for quad cores.
But, probably within two years, there will be a lot more games that will be for the quad cores (which would actually make a quad core worth owning, finally, if you're into gaming). This, in turn, will most likely mean more available quad core processors at much lower prices than they are now.
As for the heating issues, I doubt they will be that drastic in the desktop. Worst case scenario, it will result in a performance drop off.
I am currently in the process of selecting parts for my next gaming pc which I will build myself (it will be the first computer I build from scratch but I now have the experience that I feel comfortable to do so). The most important thing when you are concerned with keeping the inside of your pc cool is the case (in my opinion, the case is the most important part period). Cases that provide enough room to accommodate large fans and liquid cooling systems are what you want if you know you will be doing a decent amount of gaming (the cooler you keep your computer, the better it will perform and the longer the parts inside will last).
I am probably going to go with the Thermaltake Kandalf eATX / BTX LCS case for this next pc. I already comes with a liquid cooling system (hence, the LCS in the title[albeit it supposedly has a weak pump, which I might replace with a better one if I deem it necessary]) and it has a 360mm radiator ( 3 large 120mm fans). You don't need to get as intense a cooling system, heck you might not even need more than two 90 or 120mm fans, it all depends on what you have in there, how long you want it to last, and how well you want your pc to perform.
I hope I answered everything.
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