Is there a significant difference? For the most part, no, but it depends on entirely what we're comparing.
Phenoms and the Core 2 processors perform about the same clock for clock. Intel does hold the advantage, as I believe Phenom processors need about a 1-200 MHz advantage in clock speed to perform as well as Core 2 processor like the Q6600.
The 45 nm Core 2 Intel processors provide an even bigger disparity, clock for clock, than older 65 nm Core 2 processors and Phenoms.
Athlon X2s and the new Pentium Dual Cores (E2xxx series) are also fairly equal, clock for clock, but again Intel does hold a 1-200 MHz advantage.
The differences aren't going to significant to the end user, but Intel is the safe bet at multiple price points as far as processor goes. If you're talking about complete platforms, then AMD is even more competitive and can sometimes offer more than Intel at cheaper prices.