I also think that a key event of 2011 is the growing realization that the genome is the basic unit of interrogation. It is increasingly easier to begin to address a biological question by looking genome-wide, then drawing focus on the biological implications of a few select genes.
This paper of Salzberg et al in Genome Research "GAGE: A critical evaluation of genome assemblies and assembly algorithms" (quite recent) is very actual for our research;
"Which de novo assembler to choose in short read assembly...and more importantly how to assess which is the best for YOUR situation (e.g. the E-size as alternative/addition for/to N50."
This paper provides some ways to look at it which may be applicable to making a well-understood choice. Not just the choice of the assembler available at the server or because a collegue is using it fine. :-)