Charge counters are counters most commonly found on artifacts, where they track or increase a card's capabilities. Charge counters have no universal effect by themselves; each card explains what its charge counters actually specifically do.
Everflowing Chalice produces more mana as it gains charge counters, Chalice of the Void automatically counters spells based on the number of charge counters it has, and Darksteel Reactor wins the game on the spot once it accumulates a hefty twenty charge counters.