A conroe based (4mb cache) core2 performs clock-for-clock about twice as fast as a Netburst based Pentium D. Sometimes it's a little less, but that seems to be upholding in most of the benchmarks.
For the easiest closest (and readily verifiable) comparison, take a 3Ghz D830 (or 930), and compare it to the x6800 in Toms charts. Most of the times the conroe system takes half the time to complete the benchmark.
Obviously the chipset and memory speed have a role in this, but it's not a huge factor (although I can tell you that the pentium D performs a lot better on an Nforce4 motherboard than it does on a p965/945 and other Intel chipsets).
So then it'd be reasonable to assume that a Pentium D @ 3.5 Ghz will be a little slower than a stock E6300, albeit not more than 10-15%. Multithreaded benchmarks will show a greater difference, since we're virtually multiplying this advantage by up to 2x. From a user point of view, unless you have a top of the line video card or are a benchmark freak, I doubt you'll feel a difference. With D805s going for under 90$ and some decent Nforce4 boards well under 100$ (although they're getting harder to find), a Pentium D rig is a lot more economical than the cheapest Core2 build, if money is a big issue.
Yes, the core 2 runs cooler, faster, and you get to put that fancy "Core 2 Inside" (or whatever it says) sticker on your case. But unless you really need that kind of processing power, there are cheaper alternatives. Which are mostly the Pentium D or an Athlon64 rig (single core), those s939 chips are dirt cheap nowadays.
Cheers
p.s. If you have just read my post and happen to disagree vividly, and are preparing to write an extensive 3 page report on how "he doesn't know what he's talking about", consider the following :
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Fart.