The newer socket 939 cpu's support dual channel memory. Socket 754 use single channel memory. The addition of dual channel memory doubles the memory bandwidth of the on-die memory controller. Remember, the Athlon64 cpu's do not have to reply on a northbridge to transfer memory and graphics data to and from the cpu. This results in much lower latency and higher bandwidth.
Socket 754 cpu's support 64bit DDR SDRAM at 100, 133, 166, and 200Mhz. The socket 939 cpu's support 128bit memory at the same frequencies, so you can see the obvious advantage there. The newer socket 939 cpus memory controller also supports up to four unbufferred dimms, where the socket 754 solution only supported three. The 939s also benefit from a faster Hyper Transport bus speed (or front side bus). Socket 754 was limited to 800Mhz or 3.2Gb/sec in each direction but now 939 cpu's get a full 1000Mhz or 4Gb/sec in each direction. The 939 cpu's run cooler than socket 754 due to the fact that the socket 939 cpu requires less voltage.
So, as you can see there are several reason's why a socket 939 Athlon64 cpu may be the better buy when compared to socket 754, especially considering the price difference is hardly even $50 on average from 754 to 939 in the same class, ie 3200+ socket 754 vs. 3200+ socket 939.