It would've been here a lot sooner, but stop motion animation and working full time don't mix well.
All effects and editing were done in After Effects and almost every scene was green screen except the indoor 'light rays' scene, which was filmed practically on a set.
In order to achieve the "ultra slow" look, I had to shoot the animation at 30 frames per second, as opposed to the normal 24 fps. When viewed at captured speed, every shot looked terribly fast. But when slowed to half speed, things began to take shape. Even so, the slowed footage was still too fast, so I ended up applying a combination of "Timewarp" "Frame Blending" and "Time Remap" effects to get the final look.
The opening shot can be broken down like so: Shtubby was filmed on green screen. Then I did a live action dolly shot of my own bathroom (yes the bathroom is that fancy, at least in black and white, everything looks fancy in black and white). I didn't have a proper dolly, so I improvised with some duct tape and a model car -- the ruler was used to gauge the distance the car needed to be moved. Of course, the raw footage was pretty jittery, so I stabilized it in post.
The end titles were made with a practical effect, combined with some light compositing and tweaking in post -- I set the camera to shoot from above, focussed on a blank piece of white paper. I then wrote "Shtubby" with warm water. While the water was still wet, I dipped an ink soaked toothpick into the sides of the letters. The ink would quickly snake around, filling in the title.
I took the footage into AE and inverted the color. The title was then composited into the shot with a flourish of "Turbulent Displacement" some live action smoke and a fade in.