I am maintaining a website aiming at listing useful methods and tools for analyzing population genomics data. It is here :
http://methodspopgen.com/

If you find it useful, or want to insist on the fact that currently it can really be a mess when it comes to analyze data, please cite the associated paper (in BiorXiv now, but who knows, maybe it will be published one day):
http://biorxiv.org/content/early/2017/01/16/052761

And of course, contact me if your favorite method is not here or if you have hints that can be useful.
And good luck