The version of OS X installed on your Intel-Mac comes with special compatible versions of Flash and Shockwave plug-ins for use with your browser. Do not install browser plug-ins such as Flash or Shockwave from downloaded installers unless they are universal binaries. As of this time Limewire, Cabos, and Acquisition are available as universal binaries. Many Java apps will not work on Intel-Macs as they are currently compiled. Take great care with Java applications and Java-based Peer-to-Peer applications. If you have problems with applications not working, then completely uninstall said application and reinstall it from scratch. It would be wise to take care when migrating your systems from a PowerPC platform to an Intel-Mac platform to assure that you do not migrate these incompatible items. If you migrate a user folder that contains any of these items, you may find that your Intel-Mac is malfunctioning. In addition to the above you could also have problems with migrated cache files and/or cache files containing code that is incompatible. See also What Can Be Translated by Rosetta.
Rosetta supports "software that runs on the PowerPC G3, G4, or G5 processor that are built for Mac OS X". Keep in mind that some items that may get transferred will not work on Intel machines and may end up causing your computer's operating system to malfunction.
If you are migrating a PowerPC system (G3, G4, or G5) to an Intel-Mac be careful what you migrate. In event it does not work, follow the steps below. However, a well backed up source that includes at least two backups of all the data that are not connected to your machine will help you avoid potential issues, should they arise. The authors of this tip have not had a chance to verify this works in all instances, or that it avoids the 10.6.1 and earlier Guest Account bug that caused account information to get deleted upon use of the Migration/Setup Assistant.
The Knowledgebase article Intel-based Mac: Some migrated applications may need to be updated refers to methods of dealing with migrating from PowerPC chips to Intel with the Migration Assistant safely. A Basic Guide for Migrating to Intel-Macs