There are very many simulations of evolving populations: indeed, most theoretical research in evolution now involves some kind of simulation.
Some simple examples can be found at the PBS Evolution site.
EvoBeaker provides a sophisticated simulation package for teaching.
EvoTutor is simpler, but free.
MS and SimCoal are two of many packages that simulate the coalescent process .
Nemo simulates structured populations.
In contrast to simulations of definite evolutionary models, artificial life sets up open-ended simulations that may evolve in unexpected ways. The International Society of Artificial Life keeps a list of programs. A popular system is Avida, from the Digital Life Laboratory.