There is an app for OSX called "Bartender" that lets you hide multiple app indicators behind a single icon. I've tried looking for an Ubuntu/*nix equivalent to no avail. Does any one have any suggestions?
Ubuntu pioneered "indicators" instead of "system tray icons" as they were before in order to solve this problem. There are now a limited number of indicators that are based on function, and each indicator can represent multiple applications.
Examples: the sound indicator controls your system volume and also your music player; the messaging indicator interfaces with instant messaging, email and microblogging.
More information at: https://wiki.ubuntu.com/DesktopExperienceTeam/ApplicationIndicators
However, this is really for developers. I'm not aware of any mechanism that allows users to collapse multiple system tray icons without getting a developer to alter the program. Perhaps someone else has an answer for that.
KDE environment in kubuntu have plasma widgets having similar feature. You can define group on desktop icons.