We wrote earlier about Firefox Flicks Blender Animations. During the creation of the FoxFire entry the author has written a really good tutorial on using Blender's Sequencer and the Alpha Over effect in particular. This is a great effect and an even greater mystery to many, but this tutorial will help you understand just how to setup one of the most popular sequencing effects!
One minor problem that this author brings up is Blender's line drawing capabilities. He says:
"In my case, I had to do this to overcome a limitation in Blender's edge drawing (I wanted the snow in the scene to be drawn without edge rendering) while keeping shadow interaction between different pieces."
This isn't actually correct - it isn't a limitation it's a perk! Now, it can be a limitation if you don't want to use the simple fix. See, Blender uses the unified renderer to draw the lines onto the edges of the meshes. This produces that great hand drawn cartoon look. The problem is that Blender doesn't draw edges on every kind of material. It specifically excludes alpha materials. This is the perk/simple fix to rendering one set of images without having to composite them. Simply, just take the snow (in the case of this tutorial) mesh and give it an alpha of .999 - this isn't quite opaque of 1.0 but no one could tell! Remember not to enable Ztransp or RayTransp and it will still be opaque to the renderer. This draws lines on everything but the snow!
Now, this isn't without it's own set of limitations and that comes to play when you want to have lines on transparent objects such as glass or icecubes or anything transparent like. If that be the case then you need to enable the All button in the Edge Settings. This will treat all materials, even transparent ones, as edges to be rendered on. In that case the above tutorial will suit you just fine! :D