Generally speaking: Player's Option, Unearthed Arcana (3.5), and Pathfinder Unchained as expansions of what the D&D game could be, encouraging DMs to tailor the game rules to their specifications. Pretty much all of my work in the d20/OGL/OSR sphere owes something to these products.
I really liked Wizard Schools and Priest Spheres from the AD&D 2e in general and Player's Option in particular; I feel like Wizard and Cleric are too broad to be really flavorful, and replacing them with several narrower classes (like focused specialists and specialty priests) makes the magic characters can wield more special. I like the Wizard's school powers and the Cleric's granted powers in Pathfinder.
I liked Kits in 2e and Archetypes in Pathfinder. I... really, really like Rogue Genius' Genius Guide to the Talented (classes) series, which breaks down most of the official archetypes and some third-party archetypes down into pick-and-choose abilities, and the Genius Guide to (theme) Archetypes which presents generic archetypes that can be used with any class.
I really liked the idea of Prestige Classes in 3.X, but the execution left me cold... especially when it replaced a lot of character concepts that used to be (1st level) kits. However, Paragon Paths and Epic Destinies in 4e are a lot closer to the mark.
I liked the At Will/Encounter/Daily/Utility power structure of 4e. Especially when they added Psionics in PHB3 and Augment powers. On the subject of 4e, I loved Healing Surges.
I love the Soulknife class in 3.0, and moreso in 3.5, and especially the Dreamscarred Press version in Pathfinder.
I love the weird D&D races that are only in D&D, like the Gith, the Thri-Kreen, Tortles, the Hadozee.
I generally like the spell slot magic system, especially the way it's used in 5e.