According to DXO, the nikon d700 at ISO6400 is really 4871. The 5Dmk2? It's 3990. The Nex 5N? 4540. Nikon, Canon and Sony short change us all too!
ISO was established for film makers to standardise their emulsions so camera meters will work consistently with all brands of film. It worked very well for that era and the concept of sensitivity as labelled with well known ISO numbers (64, 100, 200, etc) was carried over to digital. But there are pitfalls in doing so.
In the digital era, each manufacturer can and will use different gain settings for their analogue amplifiers, so calling the amplifier gain setting the 'ISO' is wrong. Their concept of ISO is to match the final output from the raw converter (in camera or on the computer) with what would have been achieved had film of the same ISO rating been shot with those exposure settings.
This is all a little confusing because we expect the ISO values to yield the same brightness in RAW. But it isn't since RAW isn't considered by the manufacturer to be the final output. There is a valid reason for this (no, it's not marketing trying to short change us. Not this time anyway!). When they design the analogue amplifier, they know which part of the gain curve is most linear. By limiting the gain to just the portions of the gain curve that are most linear, they reduce amplification noise. They then compensate by increasing or decreasing the digital value from the sensor to the correct brightness for that ISO setting. In fact by doing it this way, enough noise is reduced that increasing the digital number still results in a cleaner image than gaining up the amplifier to keep the digital number unchanged. I think <speculation> their ultimate goal is to have only one gain setting in a very linear amplifier, then match ISOs simply by tweaking the digital number. This would simplify circuit design and keep parts cost down. <\speculation> Sigma tried this, but failed to achieve sufficient S/N ratio for good output at higher ISOs.
At the lower end of the ISO scale, some manufacturers, trying to keep within the linear part of the gain curve, 'understate' the ISO, then digitally reduce the brightness for the final output. This compromises dynamic range, but keeps noise low. That's why for the D700 (and some others as well) the 'base' ISO is not 100, but 200.
Sorry, a bit long winded, but hope this helps...