If you find an application that does not open or function correctly, use the steps found in Intel-based Mac: How to tell if an application is Universal to see if the application is Universal. If the application is PowerPC (not Universal), check to see if a newer version of the application exists that may work better with Intel-based Macs.
When Migration Assistant or Setup Assistant is used to migrate applications between two computers, it will bring over any applications it finds on the source computer that are not already installed on the destination computer. In some cases, a PowerPC-based Mac may have applications that will not run correctly through Rosetta on the Intel-based Mac.
For example, if your PowerPC-based Mac has X11 installed, but your Intel-based Mac does not, and you use Migration Assistant to migrate applications from the PowerPC-based Mac to the Intel-based Mac, X11 will get transferred to the Intel-based Mac but it will not open. In this case, you can delete the PowerPC version of X11 and use Optional Installs on the Install Disc that came with your Intel-based Mac to install the correct version of X11.
To learn how to use the Migration Assistant, see How to use Migration Assistant to transfer files from another Mac.