I think some of them depend on regional variations (-iño for example is something that you would hear in the north of Spain, influenced by Galician speakers).
Other suffixes may contain different inflections (-illo may contain an emotional inflection).
Dinerito vs dinerillo
Hombrecito vs hombrecillo
Also -illo may depict things that are smaller than -ito (cucharita vs. cucharilla) but there is not a definitive rule about this.
-zuelo may also contain emotional (pejorative) connotations.
The differences and connotations between them may be so fuzzy that the context would give you more information than the suffix itself and is not possible to get a proper, definitive list of the variations of significance and connotations of each one of the suffixes.
-illo and -cillo may be less common due to regional differences. Some Spanish dialects may be less prone to use certain suffixes (making even more difficult to get a definitive list of the exact connotation of a diminutive or its divergence/variance from others).