Links I really like
UCSC Genome Browser : Ubiquitous and fantastically data rich, UCSC Genome Browser is my go-to.
WashU Epigenome Browswer : Excellent 3D visualization tools as well as host to a number of consortium data hubs
Cancer Cell Line Encyclopedia : Search for your favorite genes and compare expression across multiple cancer cell lines. Very well done.
HOMER : One of the best annotated software suites, this is still my favorite semi-integrated next-gen sequencing analysis software. Bonus for being great at its original function: DNA motif analysis
Bedtools : Indispensable tool for analysis of genomic intervals/peak locations.
Homebrew : Easiest way to install and update command line software tools on Mac.
Homebrew Formulas : Nice list of software that can be installed/managed by homebrew.
Gene Expression Omnibus : NIH-funded repository for genomics data of all types
Sequence Read Archive : NIH-funded repository for next-generation sequencing reads.
deeptools : Very nice suite of tools for some ChIP-seq/RNA-seq applications; many uses!
STAR Aligner : Super fast and accurate aligner: requires high RAM for mammalian genomes, but speed can't be beat.
Bowtie2 : My favorite short read aligner (mainly because I know how to use it).
HOCOMOCO : Nice database of DNA-binding protein motifs
Firebrowse : Integration of (primarily) the Cancer Genome Atlas (TCGA) data
cBioPortal : Integration of TCGA and many other datasets
EMBOSS : Software suite that performs numerous DNA/RNA sequence manipulations
JASPAR : Transcription factor binding motif database
Software Carpentry : Learn how to code (I need to do this)