I'm gonna get lynched for saying this, but in terms of pure performance, the IPC of a 2MB L2 Core 2 Duo was on average 2.05x that of a Pentium D. IOW, take the 1.8ghz of the E4300, multiply that by 2.05, and you 3690. So a Pentium D around that clock speed on the same exact board, same ram, same hdd, etc, could be nearly indistinguishable in performance.
That said, most C2D setups came with better boards, ram, hdds, etc, and that will tend to skew the average system performance towards the C2D for sure. Eg; a PD 3.6 on a 915 board with 2GB of DDR2-533, a 160gb 2005-era hdd, and an ATI X800 would compare somewhat poorly to a C2D 1.8 with 2GB of DDR2-667, a 500gb 2007-era hard drive, and an ATI 3650.
And then there's the issue of heat/power. A PD at 3.6ghz is a damned furnace.
TL : DR - technically on equal terms there's not that much performance difference, but IRL the C2D is the better bet every time and twice on sunday.