We use a highly homogeneous set of data from 132 early-type galaxies in the Virgo and Fornax clusters in order to study the properties of the globular cluster luminosity function (GCLF). The globular cluster system of each galaxy was studied using a maximum likelihood approach to model the intrinsic GCLF after accounting for contamination and completeness effects. The results presented here update our Virgo measurements and confirm our previous results showing a tight correlation between the dispersion of the GCLF and the absolute magnitude of the parent galaxy. Regarding the use of the GCLF as a standard candle, we have found that the relative distance modulus between the Virgo and Fornax clusters is systematically lower than the one derived by other distance estimators, and in particular, it is 0.22 mag lower than the value derived from surface brightness fluctuation measurements performed on the same data. From numerical simulations aimed at reproducing the observed dispersion of the value of the turnover magnitude in each galaxy cluster we estimate an intrinsic dispersion on this parameter of 0.21 mag and 0.15 mag for Virgo and Fornax, respectively. All in all, our study shows that the GCLF properties vary systematically with galaxy mass showing no evidence for a dichotomy between giant and dwarf early-type galaxies. These properties may be influenced by the cluster environment as suggested by cosmological simulations.