You're exchanging a lower clock speed for more "cores". Unless you're running an application designed to take advantage of multiple cores, or you are running several different processor-intensive applications simultaneously the Core 2 Duo will be about 20% faster for you due to the higher clock speed (3166 MHz vs. 2500 MHz).

If you *do* run multi-threaded applications that are specifically written to spread their computation across multiple processor cores, then the Quad will be considerably faster. Way faster -- assuming the computational task lends itself to be solved piecemeal. Engineering software like finite element analysis packages benefit tremendously from multi-core, as long as there is enough RAM to keep the process CPU bound.

What will you be using the machine for?

Edit: note that some games written to support multi-core are still bound by one computational thread and thus the extra speed of the 2 core system will actually result in higher performance than the 4 core system -- even though the program is written to take advantage of 4 cores the problem it is trying to solve is not well suited to this. Unless you have a numerically intensive application or are running a server, get the 2 core chip.