Slic3r stable version 1.1.6 is out. Since last time I looked at it it now has many new options like linear gap fill, per-region settings, modifier meshes, pillars / bridge support material, model cutting etc.
Here is a review by James Bruton (known for his 3d printed costumes such as 3d printed Xenomorph). He
explains functions like improved multi-material print handling and others.
http://slic3r.org/releases/1.1.6