The iMac G5 is a solid, reliable machine.
I was the proud owner of one (until I finally upgraded to an Intel iMac).
When I owned the iMac G5, I purchased a MacBook for my wife. The C2D Intel processor in the MacBook simply blows away the IBM G5 processor in the iMac. I really noticed this when using Handbrake.
With the iMac G5, it would take around 8 hours to convert a movie to the settings that I wanted. With my wife's MacBook, it took less than 2 hours. That's when I knew it was time to upgrade (and the fact that I could run all the operating systems that I wanted to on the Intel machine).
The other factor to consider is the graphics card. I don't have hard evidence, but I am willing to bet the integrated NVIDIA card is near equal, if not better, than the dedicated ATI card in the iMac G5.
To answer your question, yes, you will see better performance with the Intel MacBook.