Here is my theoretical analysis on this stuff...
Kawasaki. Gp550 became GpZ 550, the Z was the sporty version which carried through to the Ninja series which used the Z in the model numbers (ZX600) Thus i can only assume that Z stands for "sportbike". In addition to the Z Kawi used "R" to indicate that a particular bike was a bad ass racer, i.e. 600R, 750R, 1000R, (these bikes ripped in thier day). As the AMA racing circuit competition became stiffer these "R" bikes became less and less competitive. So by the time the ZX6 was introduced it no longer carried the "R" designation as it was ANYTHING but a race bike. The ZX7 was introduced with this reality in mind and didnt have the "R" either. Behind the scenes kawi WAS involved in racing though and teh R was reserved for race prepped bikes. By the time we all began to demand a better sportbike Kawi was ready to introduce the near race ready models, ZX7R (later RR) ZX6R and ZX9R, and now ZX12R. Make s sense to me.
Suzuki began the sport/street line with the GS line (GS500, GS750, GS1100) some of these were E models and some were L models. The E models were sportier. These were "Sport Standard" bikes. Big, powerful road bikes that were popular in the day. After the "sporty demand" went through the roof the E model wasnt cutting it, so Suzuki introduced the GS-X models which was the first true "sportbike" from them. We can only assume that GS indictates the "Sporty" line and X means "even more sportier than sporty" The GS-X bikes were very popular but after the FZR yamahas and Ninja ZX models begand selling like hotcakes suzuki upped the anti with the GSX-R lineup whicj was more "race" ready than previous relatives.
Yamaha i have no clue about except the precursor to the FZR was the FZ, thus R stands for a more modern sportier model, (racer?)
Well, this is my take on history, if anyone has any HISTORICAL correction please enlighten us historian types!!!