The RuleTree algorithm allows rules to be specified by special trees (n-ary decision diagrams) stored in external files. Given the rule string "Foo", the RuleTree algorithm will search for a file called Foo.tree. A number of examples are stored in the Rules folder:

B3/S23 or Life
Conway's Life. This is the default rule for the RuleTree algorithm.

BriansBrain
An alternative implementation of the Generations rule /2/3.

Byl-Loop
A six state 5-neighborhood CA that supports small self-replicating loops. To see the rule in action, open Byl-Loop.rle.

Caterpillars
An alternative implementation of the Generations rule 124567/378/4.

Chou-Reggia-1
An eight state 5-neighborhood CA that supports tiny self-replicating loops. To see the rule in action, open Chou-Reggia-Loop-1.rle.

Chou-Reggia-2
Similar to the above rule but supporting an even smaller self-replicating loop of only five cells. To see the rule in action, open Chou-Reggia-Loop-2.rle.

Ed-rep
A version of Fredkin's parity rule, for 7 states. See Ed-rep.rle for an image of Ed Fredkin that photocopies itself.

Evoloop
An extension of the SDSR Loop, designed to allow evolution through collisions. To see the rule in action, open Evoloop.rle.

Langtons-Loops
The original loop. Chris Langton adapted Codd's 1968 CA to support a simple form of self-replication based on a circulating loop of instructions. To see the rule in action, open Langtons-Loops.rle.

LifeOnTheEdge
A CA proposed by Franklin T. Adams-Watters in which all the action occurs on the edges of a square grid. Each edge can be on or off and has six neighbors, three at each end. An edge is on in the next generation iff exactly two of the edges in its seven edge neighborhood (including the edge itself) are on. This implementation has 3 live states with suitable icons that allow any pattern of edges to be created. Open life-on-the-edge.rle.

LifeOnTheSlope
The same behavior as LifeOnTheEdge but patterns are rotated by 45 degrees. This implementation has only 2 live states (with icons \ and /), so it's a lot easier to enter patterns and they run faster. Open life-on-the-slope.rle.

SDSR-Loop
An extension of Langton's Loops, designed to cause dead loops to disappear, allowing other loops to replicate further. To see the rule in action, open SDSR-Loop.rle.

StarWars
An alternative implementation of the Generations rule 345/2/4.

WireWorld
A 4-state CA created by Brian Silverman. WireWorld models the flow of currents in wires and makes it relatively easy to build logic gates and other digital circuits. For an impressive example, open primes.mc.

References:

Byl-Loop (1989)
J. Byl. "Self-Reproduction in small cellular automata." Physica D, Vol. 34, pages 295-299, 1989.

Chou-Reggia-1 and Chou-Reggia-2 (1993)
J. A. Reggia, S.L.Armentrout, H.-H. Chou, and Y. Peng. "Simple systems that exhibit self-directed replication." Science, Vol. 259, pages 1282-1287, February 1993.

Evoloop (1999)
Hiroki Sayama "Toward the Realization of an Evolving Ecosystem on Cellular Automata", Proceedings of the Fourth International Symposium on Artificial Life and Robotics (AROB 4th '99), M. Sugisaka and H. Tanaka, eds., pp.254-257, Beppu, Oita, Japan, 1999.

Langtons-Loops (1984)
C.G.Langton. "Self-reproduction in cellular automata." Physica D, Vol. 10, pages 135-144, 1984.

SDSR-Loop (1998)
Hiroki Sayama. "Introduction of Structural Dissolution into Langton's Self-Reproducing Loop." Artificial Life VI: Proceedings of the Sixth International Conference on Artificial Life, C. Adami, R. K. Belew, H. Kitano, and C. E. Taylor, eds., pp.114-122, Los Angeles, California, 1998, MIT Press.

WireWorld (1987)
Dewdney, A. K. Computer Recreations. Scientific American 282:136-139, 1990.