Papagayo and Synfig
Designed to help you line up phonemes (mouth shapes) with the actual recorded sound of actors speaking. Papagayo makes it easy to lip sync animated characters by making the process very simple - just type in the words being spoken (or copy/paste them from the animation's script), then drag the words on top of the sound's waveform until they line up with the proper sounds.
After syncing up mouth shapes with actual sounds, Papagayo can then export the result for use with Anime Studio, their 2D animation product. I couldn't find the Linux version though. I am trying Synfig.
Papagayo is free to download and use. Sync 'till your virtual lips are sore! Papagayo is available for Windows, Mac OS X, and Linux. Download @ Lost Marble
Synfig is a powerful, industrial-strength vector-based open-source 2D animation software package, designed from the ground-up for producing feature-film quality animation with fewer people and resources. While there are many other programs currently on the market to aid with the efficient production of 2D animation, there currently is not any other software that can do what this software can.
2D Animation has traditionally been very expensive because every frame must be drawn by hand. Even with today's digital inking and painting software, the process still relies on individuals hand-drawing each frame. This laborious task is called "tweening".
Synfig eliminates the task of manual tweening, producing smooth, fluid motion without the animator having to draw out each frame individually. This allows you to produce 2D animation with fewer people while producing art of a higher quality. Download @ Tux Family
Synfig Demo Reel