Essentially these dictate how long until you can use a special attack - the smaller bars fill up faster, and you can store multiple charges.
But it should be noted that the bars doesn't affect the move's Damage Per Second though - they each deal a certain amount of damage over a certain time when activated. A more meaningful way of comparing each move is to compare their DPS.
For example with Poliwrath's special moves, Ice Punch does 13.5 dps while Hydro Pump does 20.7 dps (which is clearly superior).
But on this pokemon, to deal the most damage you should just use the Mud Shot quick attack, which does 21.8 dps - greater than any of the main moves. (The only exception would be when fighting against a pokemon type that is super Effective / Ineffective to your move type).