In the TCG, an orange damage counter is worth 10 damage (it should say right on it). Around Pokémon Black & White, the red damage counter, worth 50 damage, was added. Both counters have their damage value on them. If an attack says to put 3 damage counters on the opponent's Pokémon, the put 3 of the orange counters on. Only use a red 50 damage counter if the attack says to put 5 or more damage counters on one Pokémon.
Source: Years of playing the TCG (in the good ol' days when it was popular).