PopGene.S2: is a free software to study population genetics. It consists of eight modules, each one directed for one feature of population genetics.

PopGene.S2 is now available for download
Click here to download the first beta release. Please report any problems to
nuin AT genedrift DOT org
Modules are:

    Allele and genotype frequencies representation
    Panimixa - autosomal and X-linked case, De Finetti's parabola
    Assortative Matings - positive, negative, w/ or w/o dominance, forbidden sterile
    Drift - with "soft selection" and mutation
    Markov process
    Mutation - irreversible, two way and neutral
    Gene Flow - continent-island, island-island, F statistics, Wahlund effect
    Linkage disequilibrium and Magnitude of D
    Selection - general model and frequency dependent selection
    Effective population size
    Molecular population genetics
    Muller's ratchet

I will be adding shortly screenshots of the new beta version and a link for the annoucement list. Keep checking back.