Actually an i3 has higher OC headroom, up to 4.3-4.5GHz with an aftermarket cooler compared to about 4GHz for the Phenom II X4 965. However, the two additional cores means that the Phenom II X4 965 will probably be faster though, unless you're running an application that doesn't use more than two cores.
I would definitely go with the quad core. Intel is about 40% better on per core performance with hyperthreading accounting for 20% of that, but there are many programs that use quad cores now. The programs that don't use a quad will most likely not need all the speed the dual cores will provide compared to the Phenom.
I would also suggest getting the 955 instead of the 965 since it's slightly cheaper for almost the same proc, and it would be the same if you overclocked the 955 to the same level as the 965.
This is a synthetic benchmark, but it does show the 955(3.2ghz) beating the i5 680(basically the firstname.lastname@example.org, maybe more due to turbo boost) by about 10%. It also seems well optimized for hyperthreading, thus it probably is giving the i5 a slight boost compared to normal applications.
Right now I would just go with the max amount of cores you can get, since games will slowly use more cores.