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

Attention: PopGene.S2 is still not available for downloadIf you want to be notified when it is released, please register your email address on the annoucement list.
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.