Both are more or less the same. But based on a few benchmarks that I've seen (there aren't that many for the E6300 or E6400) at worse the Conroe E6300 performs just as well as the X2 4200+. In the best case scenario Conroe performs a bit better.
That is true for both applications and games when both CPUs are being overclocked. Personally, I would choose Conroe, but I going for the E6600.
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I would go with the E6300. The only reasons to not go with Conroe are if you can't wait (or dont want to) or don't have enough money and take advantage of the recent price drops from AMD. The E6300 will perform at least a little better than the X2 4200+