I'm proposing a tool/wizard that could publish a whole bunch of workspaces and/or custom transformers to FME Server at once. This could be a separate tool, but it could also be integrated into FME Workbench. Preferably though, it would be a standalone application that also accepts a command line. This way, you can hook it up to a SVN/Git repository for instance, so whenever you commit, all the stuff you created also gets published to the desired repository on FME Server.
It would be nice if this tool had a "recursive" option, so that it checks if custom transformers contain some other custom transformers and publish these "dependencies" as well. Right now, FME does warn me for missing transformers whenever I publish, but it doesn't check inside these transformers.