Hold on there OP, you may want to go into a bit more depth with this whole process.
You list two processors as your main points of comparision (an X2 6400+ and a Phenom 9500), but there's a lot more to consider about those two processors. the X2 is a K8 architechture. It's design is no several years old and it is based on a 90nm process. the Phenom core is AMDs newest architechture (K10 i think, since they skipped the obviously unusable K9 moniker). It is built on a 65nm process and is theoretically 10-20% faster clock for clock than K8 processors. It also makes use of the new SSE 4 instruction set and contains the TLC errata (not likely to be a problem for most users, but worth keeping in mind). This is really an apples to oranges comparison, even though they theoretically do use the same motherboards.
Also, do you already have an AM2 motherboard? If not, why are you not considering Intel processors? In that price range ($175+ USD) Intel products generally offer more performance/dollar and more overclocking headroom to boot.
Finally, what do you intend to do with this new computer. the advantages of dual-core versus quad-core largely depends on what you do with that computer. the majority of software (including most games) does not take advantage of 4 cores, and therefore benefits from a higher speed dual-core processor. However, certain activities such as video encoding can see massive benefits from 2 extra cores (80% or more).
On the other hand, quad core processors generate more heat and use more energy than dual core, so running them for 1 or 2 years can be noticeably more expensive.
This is a question that does not have simple, black and white answer. So without knowing more about your specific needs and circumstances it is hard to point you in the right direction.