Absolutely.

It's a little different dynamic from tuning cars (much easier imho because many are plug-in types) but there is certainly room to upgrade the performance of a factory standard bike. On my old GSXR I had a TRE (Timing Retarder Eliminator) modification installed and that is something generally considered for racers only (as opposed to recreational riders). In essence, the TRE is a device which allows much better throttle response in the first four gears because manufacturers make separate ignition maps for each gear (for noise, safety and emission reasons).
The TRE "unmaps" (for lack of a better word) the amount of throttle needed for shifting and changing the lower gears. The transition is as smooth as silk and ideal for weaving through traffic, riding in the city, or other stop-and-go environments. That's just one example of course. There are plenty of other mods and performance upgrades available nowadays but timing adjustment is by far the most popular (not to mention affordable).
I wanted to install a G-Pack for my ZX-12R at some point but since I am leaving for Japan soon there's not much point... And if you're wondering what a "G-Pack" is... let me just cite the following from the manufacturer:
"G-Pack is a module which has the capability to optimise the performance of your engine to a maximum, particularly during the phases of acceleration from low to mid range.
G-Pack allows for maximum torque and power with exceptional acceleration in the low and mid range permitting full exploitation of your engine power band.
WARNING : G-pack changes engine窶冱 characteristics and performance. The utilisation of the module is not allowed on public roads; its use is strictly meant for competition on closed racing tracks."
