Here are some of the entries that I played around with that I thought were interesting/cool. BTW, some of these are very picky about the browser…
Magical Bit-Recycling Tool
Man, this one chews up the CPU, but kind of cool effects. Just don't type too fast.
PixxxelChix – A 5K Porn Site
Hysterically funny. Just like the real thing (so I'm told)
cn y rd this? lrn bt ntrpy!
Very impressive (and informative) use of compression. Read the page, then be sure to 'view source'.
e-cology
Although the author challenges you to find a stable system, I think it's more fun to see how wildly you can make things swing. I could never drive either the rabbits or the foxes to extinction, but I could get them to completely disappear, with an occasional huge but brief explosion. (thanks to one of the commenters for the suggestion of de-stabilizing the system).
tableGenetics
Lets you play God/Nature and direct the evolution of html tables.
Flipmaze
You got to be patient on this one, but it's fascinating to play. Get your marble (blue) through the ever-changing maze to the exit (green) before the bad guy (red) gets ya! Just hover your mouse over the green arrows below the maze to move.
Rubik's Droid
Imagine being inside a rubik's cube. Think of this as the three-dimensional Minatour's cave. Even though you have a perfect string (it tells you where you are and which way you're facing) you'll still get completely lost. Even worse, you're supposed to push these balls around. Did I mention that the maze is "only" 10x10x10? :-)