Here is some links I visit frequently and find extremely useful:
Phytools - Blog by Liam Revell for his R packages “phytools.”
geomorph - site for the excellent R package for use with geometric morphometrics and multivariate data analysis.
Software Carpentry - excellent tutorials for basic software skills and schedule for bootcamps.
treethinkers - site for the UC Davis Applied Phylogenetics workshop, excellent tutorials.
Biostars - excellent site for questions related to NGS data and analysis.
SEQanswers - fabulous site for the NGS sequencing community.
Bioconductor - the support site for the Bioconductor suite in R
biopython - tutorials and cookbook for the wonderfully helpful Biopython.
TADW - A great compilation of bioinformatics tools (written in PERL).
Molecular Ecologist - A nice blog covering what is happening in the field.
R-bloggers - I love R and you should too. This is a great collection of posts written by R users.