In the second stage, compositing and special effects, I use the industry standard Adobe After Effects Production Bundle. On occasion if a live action clip has enough contrast, I can use the keying filters in AE to place live organisms over animated subjects, such as a darting live copepod in front of an animated micronaut or submersible. This is an effective trick to reinforce the sense of being amongst and interacting with the natural inhabitants of the micro world. I often use distortion and particle effects to give unity to the various layered Quicktime and still image elements. Wave warp gives the scene that warbly underwater look.
Motion blur adds the feel of dynamic movement to an animation layer.
Stylistically, I like Strata MediaPaint. I like the look of its effects and it's often the only tool for the ob. Having started my animation career in cel animation, I have a fondness for 2D effects. Finally, I import the finished scenes into the Media 100 editing system. There I assemble the scenes, sync animation to voice, add titles and transitions.