Even if the eMac was running its disk at just 5400 or 5200rpm, it's possible, not even just possible but quite likely that the disk in the iBook is on its last legs and has had its performance degraded since it was new.

Every time I put an honest-to-goodness brand new hard disk into a system, especially one that's used or from several years ago, the system immediately becomes far faster -- not only because of a fresh OS install or the inherent defragging involved in imaging an OS to a new disk, but because the new disk (even if it has the same specs) is just faster -- because of a few years of development in disk technology, and because it's not dying.

Desktops don't move around very often so their disks (again, anecdotal experience) don't degrade as quickly, I've found.