Would it have been too much for Apple to warn me it would wipe out all my pre-Intel programs when I updated to Lion?

Wiped everything out. Disaster. No warning....

You can redownload iTunes pruchases by:
iTunes Store: Transferring purchases from your iOS device or iPod to a computer
The iPod backup that iTunes makes during every sync and and as the a early step of an USB update does not contain synced media like apps and music. It has aloways been that way. If rhe synced media is not in your iTunes library when you do the restore it can't be synced to the iPod during a latter part of the update. See:
iTunes: About iOS backups
iOS 5: Updating your device to iOS 5

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