Makerware still uses skeinforge. They have an alternative slicer with it but it's also very slow. They've also gone dramatically closed source with makerware, and appear to be violating skeinforge's agpl3 license.
Slic3r has been improving at an incredible pace, you should try the latest one.
MakerWare can use both Skeinforge (highest quality settings) and Miracle-Grue (medium and low quality settings). We are still in Beta, so interfacing slicer engine (like slic3r, netfabb, ) is still underway.
The conveyor task engine is Open Source. So if you want to write your own plug in slic3r (or anything else) first, go for it!
Slic3r has been improving at an incredible pace, you should try the latest one.