Clank doesn't do much. For most of the game, he sits on your back, letting you use the helicopter or rocket boost, depending on which you have equipped. (These let you long jump and highjump, as well as float slowly. Basically they give you Mario powers)
There are, however, some missions where clank gets his own challenges alone, and can control up to four smaller robots Pikmin-style. In GC and UYA, there are also 'Giant Clank' missions involving smashing lunar cities. Fun stuff.