There are an annoying numbers of variables in the mix (sorry). I too run a 1st-gen, Intel-based MacBook Pro. I've noticed appreciable swings in sound quality when all I've done is an OS update. It seems more pronounced and frequent across 10.5 and 10.6. Same goes for iTunes updates.
When you moved to your Intel Mac, you definitely got a different a different audio chipset. Another thing to not like is that Apple is notorious for rolling line changes on hardware, and not telling anybody. I've found this out only because I was comparing Apples to Apples, and having isolated/tested for every other reason, I opened the machines up to see if anything was different.
Lark: Hadn't heard that about the Mac Mini. Off the top of my head, the Mini would probably sound better because it does not have the battery charging circuit. On occasion, and depending where the battery is on its charging cycle, my MacBook Pro generates audible, high freq. noise when plugged in.