Actually, good Clerics are generally better at "counterspelling" than Wizards or Sorcerers.
Cleric studies several Silence spells as a second level spell. Cleric studies several Dispel Magics as a third level spell.
If going against normal types, the Cleric can swap these spells out for cures.
If going against low level magic types, the Cleric can ready Dispel Magic (saving the more potent, in most cases, Silence).
If going against high level magic types, the Cleric readies a Silence spell. Yes, it will not stop Silent Spell metamagic spells, but it will stop virtually everything else, even extremely high level spells.
If the Cleric runs into a Sorcerer with the Silent Spell feat, s/he switches over to the Dispel Magic (or Greater Dispel Magic at higher level) spells.
This is about the best counterspelling combination available since no actual counterspelling is done.
Real counterspelling tends to not be used in the game at all, at least in my experience.