Dwarf Fortress: your dorfs all have "labors" that can be set on or off. They will perform tasks that the player sets based on their skill level relative to other dorfs with the same labor enabled, and will build up skill in those labors over time, and there are dozens. Some skills level up very quickly (mining, cooking) others very slowly (surgery, siege engineering). It's an interesting mechanic because it adds a massive layer of depth to traditional RTS classes and a lot of economic and strategic consideration.
Golden Sun: throughout the game you encounter creatures called Djinni. They correspond to the 4 alchemical elements, wind, earth, water, and fire, and they have their own stat increases and penalties that a character incurs by equipping them, which can even amount to changing the character's class. There's a lot of experimentation there, and I like that (because apparently I can't go a day without bringing up Golden Sun here).
Children of Mana: while really rather a forgettable entry in the Mana series, it did have a really neat class system. Your characters all have a grid, and you can change the character's abilities by placing gems in the grid. The effect of the gem was based both on the position in the grid and on its position relative to other gems. Throughout the game, you would acquire upgrades to the grid's size.
Golden Sun: throughout the game you encounter creatures called Djinni. They correspond to the 4 alchemical elements, wind, earth, water, and fire, and they have their own stat increases and penalties that a character incurs by equipping them, which can even amount to changing the character's class. There's a lot of experimentation there, and I like that (because apparently I can't go a day without bringing up Golden Sun here).
Children of Mana: while really rather a forgettable entry in the Mana series, it did have a really neat class system. Your characters all have a grid, and you can change the character's abilities by placing gems in the grid. The effect of the gem was based both on the position in the grid and on its position relative to other gems. Throughout the game, you would acquire upgrades to the grid's size.