I'm no scholar when it comes to these chips, but I've read enough reviews in the past few days to say, "Forget talk of L2 cache, that E6600 is just plain faster."
The tests are conclusive: in challenge after challenge, the E6600 topped AMD's finest, and that X2 5000+ isn't AMD's finest. I must say here that I'm referring mainly to performance in games, which is what matters to me -- for other uses, I expect you'd see similar results, but I can't say for certain.
Furthermore, the Core 2s (E6600) are said to run far cooler than the AMD's, and also much quieter, which is always nice. The cooler part, in addition to who knows what else in that chip's architecture, means that the Core 2s have been shown to be phenomenal overclockers, so if overclocking is something you do or would consider, it appears there is, again, no contest.
The only logical reason I can see for picking up that 5000+ now or in the near future is that the price has been said, in various publications, to be on the way further down. So while the E6600 is likely to run you about $335-$360 now, I wouldn't be surprised if you couldn't pick up a 5000+ for about $280 soon.
That said, is something like $50-$80 difference worth it to you?
Of course, I'm biased, I just ordered an E6600 today, but that bias is the result of the overwhelming evidence out there now that Intel has the performance war licked...for now.