Ok my new favourite feature about samtools mpileup is that you can make use of the bam indexing to specify regions you wish to do mpileup on (now I can easily max out that 250 core system in shared HPC resources! )
Calling SNPs/INDELs in small regions (see http://samtools.sourceforge.net/mpileup.shtml )
Random position retrieval that works. One of the most powerful features of mpileup is that you can specify a region with -r chrom:start-stop and it will report pileup output for the specified position(s). The old pileup command had this option, but took a long time because it looked at all positions and just reported the ones within your desired region. Instead, mpileup leverages BAM file indexing to retrieve data quite rapidly: In my experience, it takes about 1 second to retrieve the pileup for several samples at any given position in the human genome. Multi-sample, rapid random access has lots of uses for bio-informaticians; for example, I can retrieve all bases observed in all samples at a variant of interest to look at the evidence in each sample.