Like Bob said, you'll have to test it. Assuming everything except the CPU is the same, then it comes down to what software you're using and what codec you're encoding to. Some codecs are multithreated, and will be able to take advantage of a quad core system very effectively. Other codecs are not multithreaded, and so will only use one core, no matter how many you have.
I will say that since parallelism seems to be here to stay, and is making its way into video cards and just about everything else; odds are you will be seeing more and more multi-threaded software. Over the long term, I would say a quad core chip likely has more staying power, but it's always a gamble on whether or not things will reach that point before you want to get a new computer. Writing a program that is designed to work well across multiple cores requires a completely different way of thinking about writing computer programs. So until someone comes up with a system for automatically distributing the processing load across cores in a dynamic way, it could be a good while before you see a lot of everyday software that will really even be able to take advantage of a dual core CPU, let alone a quad core.
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