What is a counter in Yu-Gi-Oh for example an a-counter?

Answer 1

A counter is a marker placed on a card. You can use what you want to represent it - a bead, a die, a coin, it doesn't matter.

What the counter does is determined by an active effect that tells you what it does.

Spell Counters for example do different things depending on what they are placed on. On Pitch-Black Powerstone for example, the Spell Counters don't 'do' anything, just can be transferred to other cards that can use them. On Breaker the Magical Warrior however, one increases his ATK by 300, and allows him to use his S/T card destroying effect.

The same goes for other cards, like A-counters, Venom Counters, Hyper Venom Counters, they only do something when a card in play tells you what they do. So even if a card has an A-Counter on it, or a Venom Counter, the counters do nothing without an active effect saying what they do, like Alien Grey, or Venom Swamp.