Jobs demo'd Podcasts with chapters in iTunes, so how about his keynote with chapters too?
WWDC 2005 Keynote with chapters
Here's Apple's tutorial on how to make chapters - QuickTime has had this feature for over 10 years, so we can only wonder why Apple don't use it themselves.
As to the topics of the speech, running bits of Mac OS on Intel has been going on since 1996; the tricky part of it is getting endian-flipping right when serialising to disc, as Greg Chapman's technote from 2000 makes clear. You don't know you have it right until you have written and read files both ways between different endian architectures.
Chapters in podcasts is a good idea, but this needs a bit more to be actually useful - it needs iPod support (the skip button going to the next chapter), and we need the info back from the iPod about which tracks and chapters have been played, and which ones skipped. With that there are a lot of interesting things that can be done.