I'm building a gaming pc and was hoping someone more knowledgable with cpu's could help me out on which would give me better performance and fps while gaming. The Intel Core 2 Extreme QX9650 or Intel Core 2 Quad Q9550? I'll mainly be playing World of Warcraft and COD4.

I doubt you will OC any of those chips so just go with the Q9550, you'll be able to play CoD4 and WoW maxed with any of the CPU.
 
But to answer your question, qx9650 is better.
You do know what are extreme cpu right?

B88, as Madam Bytch noted, the faster processor would serve you best in gaming.  However, I'm sure you know that most games today can not exploit a quadcore.  To get the very best gaming you'd want a better graphics card first, followed by a CPU that won't bottleneck that card.  The QX9650, being an Extreme processor is easier to overclock due to its unlocked multiplier...but you pay a lot for the convenience.
 
So, to answer your question, the QX9650 would be better, its faster at stock, and it overclock easier.  ...but its so much more expensive that its not really the intelligent buy unless the money is irrelevant.

I have a QX9650 and play crysis with all settings at very high on a 19" CRT (yes I am going to upgrade the monitor soon) and basically the game can't load all 4 cores to 100%, not even at stock speed of 3Ghz. I have dynamically oc'd mine to 3.7Ghz and had it at 4.2Ghz untill recently. This cpu is an overclockers cpu, not only is the unlocked multiplier a saviour when the fsb won't budge (I have had my multiplier at 12) but the multiplier has a divider of 0.5 so you can have say 10.5x400Mhzfsb which is also another great advantage.
 
If I was you I wouldn't even bother with the Q9550, get a Q9450 for some future proofing and spend some money on a crossfire or SLI setup. Personally I'd opt for the Nvidia GPU's because of the prompt driver upgrades and support you get. Also the money you save would go  towards a great monitor.

All benchies show that the E8400 outperforms those quads in all games, and is around $190 on the Egg.  So, if money is a factor for you, you could get the E8400 (or even the E8500) and spend the rest on graphics.

Unless your a good overclocker go with the Q9550 but I will also side with what DXRick said about the E8400 which is a very nice cpu at stock and also overclocks very well.

DXRick nailed it.

Quad are better in few games like supreme commander and flight simulator. If you plan to keep your computer a few years, I would go with a quad.
 
And the offer some other advantage over dual too. Faster unzipping/encoding ect ect. You can always have some other programs in the backgroud without losing performance.