well, i haven't used the amd64 release of FreeBSD, so honestly i really wouldn't know
maybe someday, but i have yet the need for that kindof power in a BSD box.
as far as the whole ibm and apple thing, i'm sure the amd chip is very much amd, however i think it's the basic architecture they share. amd obviously took the basics and went much further with it, something apple really isn't in a position to do.
i'm sure the g5 is a neat chip, but i'd say the amd outclasses it in a few places. but, all in all, for most applications the chips are fairly similar. it's not until you get into some serious stuff, like jargantic photoshop stuff, 3d rendering and movie crunching where you'll notice a large difference, from what i've seen.
the only thing that torqued me off is the marketing pitches used by apple about the g5... that was rather dissappointing.