What are examples of genes succesfully reproducing in ways that is in conflict with helping the individual creating offspring
The prototypical example of this is t, whose existence was predicted by Robert Trivers and featured prominently in the Selfish Gene.  The current dominant point of view in evolutionary biology is that genes act in their own interest and even the 'self' is just a manifestation of the gene's reproductive properties.  

t is a locus in some male mice. The t gene characterizes very well the selfishness of a selfish gene.  While most paternal genes are found in 50% of offspring, t is found in over 3/4 of offspring.  Somehow it manages to reproduce at the expense of the other loci in the male mouse.  t itself is not known to convey any advantages to its host organism.  the males tend to be smaller and sometimes even reproductively disadvantaged.  

Does that go some way to answering this question?  

Animal behavior such as cheating or adopting are often interpretable as reproductive advantages.  Killing the best and brightest definitely are to the advantage of those who are doing the killing.  This SNL Skit has always said it best to me. "... and now I am smart!".  Such kill offs so rarely include killing one's own offspring.  I'm not sure they can be called in conflict with reproductive advantage.  EO Wilson's essay "On Human Nature" does a reasonable case for saying that wars and famines are in fact produced by evolutionary advantage, however cruel and ugly they may be.