What about Power Functions motor, S size?
Only in 2012 the L-motor was released. The M and XL motors where released in 2007. That is a gap of 5 years where people were even more confused about the size options...

Anyway, no smaller motor with power functions

However if you are willing to go with the 9V system (possibly with conversion cables), there's the mini and micro motor, standard motor is also a bit smaller in length.

More info here:
http://www.philohome.com/motors/motorcomp.htm