Because of a bug in Unity, I try to avoid using regular notification area icons and only use AppIndicators. Unfortunately, Shutter (an amazing screenshot tool for Linux) doesn't have an Application Indicator and it doesn't seem like it will be getting one any time soon (because there are no Perl bindings for AppIndicator).
Since I want to learn Python and because Shutter is an application I use daily, I've decided to create an external AppIndicator for Shutter. The code is probably very bad since this is the first time I write something in Python but it works for me so I wanted to share it with you.
Add the WebUpd8 PPA and install Shutter Indicator using the commands below:
sudo add-apt-repository ppa:nilarimogard/webupd8 sudo apt-get update sudo apt-get install indicator-shutter
You can also manually install the .deb if you don't want to add the PPA - download it from here.
Since this AppIndicator is not built into Shutter, you'll have to run "Indicator-Shutter" from the menu instead of the actual Shutter application. Alternatively, you can search for "Main Menu" in Dash, go to Accessories > Shutter and edit use "indicator-shutter" as the executable for Shutter. But that's not really required if you remember to simply launch Indicator-Shutter instead of Shutter.
Known issue: The Shutter Indicator will start Shutter without a notification area icon (that's the intended behavior), but if you exist Shutter and start it manually, you'll get both an AppIndicator and a notification area icon so try starting shutter from the AppIndicator only or don't exist it (clicking the close button won't quit Shutter so that's ok; only the File > Quit option will exit Shutter).