Thomas Phinney, Adobe's Product Manager for Fonts & Global Typography, listed fonts included in CS4 and noted that some CS3 fonts are not in CS4. While this only effects new installs, it could still bite people expecting to see certain fonts in any circumstance. He says:
"Typefaces you might have seen in CS3 that aren't in CS4: Arno Pro, Bickham Script Pro, Garamond Premier Pro. Further typefaces bundled with InDesign CS3 but not InDesign CS4: Bernhard Modern Std, Caflisch Script Pro."
Care might be warranted in some cases; for example Garamond Premier Pro is now selling for $199.