What is the most genetically simple organism except viruses?
Mycoplasma genitalium was one of the first full bacterium genomes sequenced and since its a symbiotic organism that lives on the moist and warm genital skin surface it doesn't need as many genes as many bacteria.  It has a 582 kbp genome sequence with only 521 genes.

But that is so 1995.  

The 159 kbp genome of Candidatus carsonella was published in 2006. It is thought to only contain 182 genes.  Its an endosymbiont of some sap eating insects.  

But the current record holder, published this year, is Nasuia deltocephalinicola, discovered survey of insect endosymbionts, has only 112 kbp in its genome. Smaller than some viruses.  It's thought to contain 137 protein coding genes with 29 tRNA genes, so its not a lot smaller than Carsonella in terms of gene count. 

There's no reason to expect that this is the minimal viable genome by any means.  I'm sure this response will need revision in a year or two. 

M. genitalium has become the model system for minimal genome work.  Many of these other bacteria might be difficult to culture, molecular biology lab techniques might have to be developed, so hopping onto newly discovered bacteria isn't always the best idea from a standpoint of producing science.  It does suggest that M gentalium doesn't need all of its genes!  A possible cause for these extra genes might be a more complex immune response in human beings where its found.  It might also be because of the symbiotic requirements of insects is simpler.