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So far... the author's favorites (in no particular order):
Invader Fractal
I enjoyed the space filling algorithm of the emotion fractal so much that I kept inventing objects to place within it. However, inventing the 'invader' can't actually be claimed since the system has been there all along...
Sea Thing
Floaty majestic creatures with bioluminescent appendages are pretty amazing. The title of this makes me laugh every time I read it. I am childish.
fake space Text Space
Flying through a virtual construct of type is fun. Even in this humble setting.
emotion fractal Emotion Fractal
This algorithm gives me hours of satisfying programming experience.
network evolution Network Evolution
A good substitution system is both simple and intricate. Wolfram's enumerated thousands of them as applied to spatial networks in Chapter 9 of A New Kind of Science. Very fun stuff.
deep Lorenz Deep Lorenz
This abstracted take on the classic attractor encourages me to research chromium engraving.
walking things Walking Things
A good take on an old idea. The kids love these little guys! And so do I.
orbiting networks Orbiting Networks
Watching the transcribed paths of nodes in a hierarchical orbiting system makes me happy.
Tornado Code Poetry
Slamming words around has always been an enjoyable way to pass the time.
Celestes : 2000 Calendar
Inspired by the compendiums of illustration published by sir Edward Tufte.
Pond Code XML Interface
This interface was my first successful visualization of XML using a single instantiating object.
Root System
Just plain cool.
Growth Identification
An endless substrate in which to grow and show data structures.
Walking Bug Generator
These little guys are pretty dumb, but their combinatoric construction process makes them attractive.
Diffusion Limited Aggregation
This is a good example of a chaotic system that generates surprisingly recognizable forms.

Randomly Connected Binary Network v5 (Self-Organization)
I played with this for weeks.

Maeda Study: A Game of Navigation Skill
I can get to level 13, how about you?
Attractor Sets
Although I've never quite found a suitable application for this system, it does seem to be an interesting concept.
Nine Block Pattern Generator
If I had the time to cover an entire wall with these things, it would be so.
Storm Front
Who isn't especially fond of the recursive form?
commercial free open source since 2012 positive attributation