Joystiq's regular RPG columnist Rowan Kaiser argues Wizardry VII has the best ever RPG class system:

One of the defining characteristics of the role-playing genre is its class systems. Although not every RPG has classes – Fallout or The Witcher, for example – some tend to be notable for their lack of classes. In some games, class is a single, permanent decision at the beginning of your adventure, and in others it's something that can be manipulated throughout. In most cases, though, it is the single most important aspect in determining how your characters interact with the game world. Thieves sneak and back stab, fighters charge in and absorb damage, snipers shoot from a distance.

The most impressive class system I've seen in an RPG is in 1992's Wizardry VII: Crusaders of the Dark Savant (as well as its less well-known predecessor, Bane Of The Cosmic Forge). What initially appears to be a straightforward, rigid D&D-style system is given massive depth by two things: the importance of racial base stats in determining class, and a dynamic system that allows for both massive improvement and possible disaster. It's possibly the most in-depth system I've seen in any RPG, and one that I wish was more well-known.