When I first got my hands on the Axion Lensflare fillter for tS2, the first thing that came to mind was to do a Babylon 5 style animation.
Running lights was something that I had wanted to try for some time, so that was the first thing to tackle. Keyframing color intensity was the first thing I attempted, but that turned out to be an exersize in frustration and didn't give me satisfactory results. I eventually came up with the idea of using an animated texture. I made a very simple animation in Premeire consisting of a blurry red band on a black background that moved from top to bottom. A bunch of small light objects were then booleaned together as one big array, and a planar UV map applied to it. The texture values for the lights were Ambient 0.2, Shine 0.7, Rough 1.
The ships in 'Bay' are pretty lame models - I made them by sweeping, point editing, and beveling a cube - a real quicky. For the sake of performance, I usually use very simple models when animating. When I'm satisfied with the motion, I then save the path to the Path Library and attach it to a more complex object. At one point I decided to slap a texture on the ships so that they matched the coloration of the scene. I liked the way they looked, so I decided to keep them. It's amazing what texture and bump maps can do for an object.
It is essential not to use Cinepak compression on animations with lensflares. Cinepak is normally my codec of choice, but it tends to destroy all detail in bright areas and makes flares look really crappy. So for 'Bay' I used Indeo at 100% quality. It doesn't play back as smoothly as Cinepak does, but it looks a heck of a lot better.