The most recent beta (1.42+) versions of Slic3r PE (Prusa Edition) now include more intuitive controls for customized supports. You can download the latest build of Slic3r PE from GitHub.
You are now able to add primitive shapes like cube, sphere, cylinder, etc. You can manipulate the shapes by scaling, rotating, and moving them on X, Y, and Z. This allows more fine tuning of what supports you do and do not want to include.
The horse model below has elements that need supports and elements that most likely do not need supports.
You can see what the default settings produce in terms of supports below. There are supports across almost the entire bottom of the horse as well as some for the mane and ears.
By adding some primitive shapes as support blockers we tell Slic3r where we do not want supports.
Manipulating that element lets you move and change its size and place it exactly where you want to block supports from being generated.
Once you’ve placed your support blocking element you can add more until you get the supports that suit your needs.
The end results, after slicing, are supports exactly where you want them rather than relying on Slic3r’s best guess of where supports are needed. This can save plastic, but more importantly, it reduces the amount of work you need to do after finishing the print. Supports can also leave rough surfaces on models that you print.