Currently elementary OS Freya uses
gnome-screenshot as its default screenshot utility.
This has an annoying bug were screenshots of active windows will show the background around the border.
I've found that screenshot-tool, an app built for elementary OS, solves this while integrating nicely with the system.
How can I change the default application that launches when PrtScrn is pressed, from
screenshot-tool you can add its PPA, as instructed in the elementary-apps blog:
sudo apt-add-repository ppa:fabiozaramella/screenshot-tool && sudo apt-get update sudo apt-get install screenshot-tool