in R/S/E/FR/LG, special/physical is determined by the move's type:
physical:
Normal
Fighting
Flying
Bug
Poison
Ghost
Steel
Rock
Ground
(examples: Hyper Beam, Focus Punch, Earthquake)
special:
Water
Fire
Grass
Dragon
Dark
Psychic
Ice
Electric
(Examples: Ice Beam, Fire Punch, Psychic)
in D/P, this is no longer true. physical/special is based on the move itself.
examples: Hyper beam becomes special, and fire punch becomes physical