I usually hear 個 referred to as a general purpose counter (which is how it is used in Chinese) similar to hitotsu, futatsu, etc... I just read a source which claims that it tends to refer to 3-dimensional objects and contrasts with 本 in this way:
ni-hon no nasu = two (long) eggplants
ni-ko no nasu = two (round) eggplants
Is this correct or would "ni-ko no nasu" be better left as "two (unspecified) eggplants"?