To answer my own question, I have two systems I tend to love. Job classes are the ones I usually mention. If the game has a robust job class mechanic, I tend to like the customization options pretty well. FFV, FFXII:TZA, FFTactics franchise, Tactics Ogre/Ogre Battle, and Dragon Quest are all great series for these types of things. It's very rare that I find a game with a class system that I don't wind up liking. I can only think of maybe three games where I have issues with the class systems.

My other favorite, and the one I prefer for more character driven pieces are hybrid systems where the party has a set class but there is an ability to customize and change them. This can range from light affairs like FFVI and IX where the customization options are lighter and don't dramatically change the characters to games like Suikoden III/V and Breath of Fire III/IV where the cast can actually be dramatically changed with enough effort or even made even more specialized if you choose so. Though I do find it's hard to find these types of systems, or at least ones that get it right.