I'd love to see FME have the ability to push modules/custom transformers/bookmarks up to the server that automatically gets copied to all workbenches on the server containing that module. If you could create a bookmark in the usual way and then save it as a module. Then on the push select if you want to push the entire workbench to the server or just individual modules. That way if you have lots of shared functionally between workbenches you can push to all the FME workbenches in one hit rather then making multiple small changes.
We have multiple complicated workbenches that share functionality but wouldn't want to have just one workbench doing everything due to unwanted complexity. However, ensuring bug fixes and small changes are equal across all the services can be painful.
If this could be put in place along with a more GIT based versioning system FME server would be a lot easier to work with.