I find an RSS feed to the bioinformatics section of SeqAnswers to be pretty much invaluable. And a subscription to the mailing lists for all the tools I use - MAQ, bowtie, bwa, etc. etc as well as an eye on bioc-sig-sequencing for R/BioConductor related stuff.

The thing I have found recently in the field, is that there is no such things as best-practice established, a tools ecosystem that has not yet undergone enough selection to produce clear winners for most NGS tasks and there is a paucity of documentation. I think this is to be expected in a rapidly moving field, so there is currently no substitute for 1) experience and 2) an eye on what everyone else is doing.

Most of my recent 'oh really?' moments have come chatting with other bioinformaticians doing similar analysis with similar aims (in my case variant detection from exome capture).

Just my $0.02

EDIT: There's also a recent set of summary papers in Briefings in Bioinformatics

It might be useful for you to check out the GALAXY 'NGS TOOLBOX' at http://main.g2.bx.psu.edu/. It contains a selection of analysis tools for different aspects of NGS, e.g. variant analysis, ChIP-seq. There is also a section for QC (quality control) of reads, which is an essential step. This is only a small selection of what is available, but it will give you a feel for what can be done. You may also find some of the GALAXY "Quickie" movies of use.

You may also want to familiarise yourself with the SAM/BAM format, which makes data analysis and storage easier http://samtools.sourceforge.net/.

In terms of viewing data I like to upload my data in UCSC browser http://genome.ucsc.edu/, but other stand alone browsers such as IGV http://www.broadinstitute.org/igv/ or Savant http://compbio.cs.toronto.edu/savant/index.html have their own strengths.

Have fun!

Also have a look at the Bioinformatics NGS virtual issue. It keeps track of a range of latest tools.