There's bad news and then there's good news.
The bad news is that the US Department of Labor link noted here no longer works. I discovered this when I was contacted by a Ph.D. student named Alan who came across the post.
I called the DOL to ask what was up. The person there, clearly reading a script, referred me to the Bureau of Labor Statistics. That person, confused by why DOL referred me there, passed me on to the U.S. Census Bureau.
The Census guy told me about this great program called the State Data Centers. Specifically he mentioned one in Missouri that has a cool database:
1. Click on the link on the right of above page to GEOCORR 2K.
2. Pick a state or states. (The Census guy I called tried NY.)
3. Select one or more SOURCE codes. (He picked the MSA). Select one or more TARGET codes. (He picked 5-digit ZIP, which are actually ZCTAs).
4. You need to pick a weighed variable. (He picked as 2000 Pop census). He picked CSV, and Codes and Names in both category.
5. Then run it. Then download it.
(I haven't tested it, but Alan probably wanted to flip what I got by putting ZIP on SOURCE and MSA as TARGET, which may be more like his goal.)
Still, since GEO IN GEO doesn't work on the American FactFinder for this purpose - for good reason - I really liked this solution. Not so incidentally, one can use this tool for other calculations as well, down to the block level.