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AlephNeil comments on Your Evolved Intuitions - Less Wrong
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I understand 'the selfish gene theory' to be the idea that we should expect to see genes whose 'effects' are such as to cause their own replication to be maximized, as opposed to promoting the survival/reproduction of the individual, group or species, whenever these goals differ.
This is almost a tautology, modulo the tricky business of defining the 'effects' of a particular gene.
I don't see how the existence of epigenetic inheritance has anything to do with it, especially as the selfish gene theory doesn't depend on genes being made of DNA, only that whatever they are, genes can preserve information indefinitely.
Genes just aren't as much of the story as we thought they were. Whether or not a gene increases fitness might depend on whether it is methylated or not, for example. Until recently, we didn't realize that there could be transgenerational transmittance of DNA methylation patterns due to environmental factors.