The performance depends on the application. In a multithreaded app like some new games, or photo / video editing software, the program is able to take advantage of the extra resources. Some apps only have support for a limited number of cores (i.e. a benefit from going from 2 to 4 cores, but not from 4 to 6), so it really depends on the application. If you are asking about a specific case, please give some more information. In general, I would say that most new applications would benefit from more cores, but older applications would benefit from higher clock speeds.
If you are comfortable with overclocking, the chip with more cores can be overclocked to more than the stock speed on the chip with fewer cores (especially with an AMD quad core over dual or triple, since the dual and triple cores are crippled quads), giving the best of both worlds.