Ok,
the first thing I see is.. 2 pass encoding. You dont need that on an all digital rip. I think. I could be wrong, but I think that that was included for ripping straight from the DVD. I think if you're doing it straight from your HDD that it doesnt matter, but someone else please feel free to correct me if I'm wrong.
As for the difference between an MBP and a PB.
I have to belive that it was one of 2 things. Let me explain why.
I had done star wars 3 a day before I sold my 12 powerbook. It took several h ours. Well then i had sold it, and forgot to copy it off.
Imagine my surprise when I came back to the MBP and did it and it took like 40 minutes. There were only 2 things different at that time.
One was the new MBP. The other was the universal build of handbrake. So it's got to be one of the 2. I do not know which, or if its the combo of the 2. Either way I don't think you have a way to speed things up, because both reasons, one way or the other, break down to having the Intel chips in your system. You've still got the G4.
Aside from that I don't really think there's anything you can do. Aside from getting a windows box and finding an OSx86 build out there from someone like Maxxus, or selling and buying a new intel Mac, I hate to say it but I think you're stuck.
But dont take my word for it, ask the other guys. But like I said, watch here and I'll start posting some results of my tests later this week.
So you know, I'll be testing it with an MTR rip of Chronicles of Narnia: The lion, witch and wardrobe. I'll try different configurations and let you guys know.
Good luck.
And hey, if you need to, PM me and I'll give you my skype info and we can talk.