It actually depends more on the amount of customization you have in Windchill.
OOTB features neednot be tested for functionality testing since PTC spends considerable efforts in testing those. Based on customization, you then have to diverisfy into UI testing, Performance Testing, Functionality testing.
If you have third party applications integrated with Windchill, you will have to consider testing to and fro transactions. if you have considerable time and resources, you can think of unit code testing during development phase using jUnit.
If you are in starting phase, start identifying customization and write test cases for the same. Based on resource and time availabilty, decide where you can have automated testing and where manual testing is required.
-Nitin