In the short term it's likely there will be core services and APIs that have been re-optimized for 64 bit. So for instance, right now, C2D processors running at the same clock speed as CD processors show about a 5-10% speed advantage. With Leopard and further refinement and at least some OS-level 64-bit code, it is likely there will be a slightly bigger margin of difference between the CD and C2D, probably especially in situations involving relatively intensive computing, lots of multi-threading, lots of memory usage, etc.
Beyond that, it's likely the same effect will happen with software...meaning the software would also show some differential advantage on a C2D above and beyond what it shows now. It's also possible that eventually software could be released that is 64-bit only. But that software probably won't be out anytime soon....