As none of the other solutions mentioned satisfied me, I wrote a script that uses WinSCP to sync local directories in a project to a FTP(S)/SFTP/SCP Server when eclipse's autobuild feature is triggered. Obviously, this is a Windows-only solution.
Maybe someone finds this useful: http://rays-blog.de/2012/05/05/94/use-winscp-to-upload-files-using-eclipses-autobuild-feature/