FME Server can use shared custom formats, coordinate systems, and transformers in the same way that FME Workbench does. Custom formats and transformers can be published to FME Server for use within a specific repository.
An FME Engine used by FME Server can have a shared resources directory defined for it based on the parameter FME_SHARED_RESOURCE_DIR in the <InstallDir>/Server/fmeEngineConfig<instanceName>.txt
The value for this parameter might look like this:
FME_SHARED_RESOURCE_DIR "C:/Apps/FMEServer/Server/resources/shared"
Within this directory you can create subdirectories for any shared resources as follows:
Transformers
Formats
CoordinateSystems
See Default Paths for information on FME shared resources.