On certain pages---and only certain pages---of my LaTeX-written dissertation, sub-pixel anti-aliasing was strangely unavailable. On these pages, where I'd embedded PDFs created in Illustrator, the print quality would also suffer. And this behavior only appeared in documents generated on one computer, which has pdftex-1.40.12; not my other, which has pdftex-1.40.11. Moving the PDF file from one computer to the other preserved the behavior of that PDF.
After a little hunting, I determined the problem to occur only when Illustrator saved its PDFs in a CMYK color space, which were then embedded in the newer pdftex-generated document. Telling Illustrator to use an RGB color space for that document fixed the problem.
The things you learn as a nuclear engineer.