The first idea that comes to mind is high level class abilities that are both mechanically and narratively meaningful. The best specific example I can give is the 20th level monk ability from 3.5e:
Perfect Self
At 20th level, a monk becomes a magical creature. She is forevermore treated as an outsider rather than as a humanoid (or whatever the monk’s creature type was) for the purpose of spells and magical effects. Additionally, the monk gains damage reduction 10/magic, which allows her to ignore the first 10 points of damage from any attack made by a nonmagical weapon or by any natural attack made by a creature that doesn’t have similar damage reduction. Unlike other outsiders, the monk can still be brought back from the dead as if she were a member of her previous creature type.
That's a highly meaningful class ability that shows true change and progression for the character. By comparison, a 20th level 5e fighter gets an extra attack, and a 20th level wizard gets more spell slots. Yawn.
The second mechanic that comes to mind is damage reduction for monsters. This mechanic essentially sets an epoch where players switch from being at a disadvantage to having equal ground with their enemies. When you first get access to magic weapons (or silver or whatever material is needed) it helps tell the story that the character is now advanced enough to more easily face a threat that was once a major hurdle.
Two more examples from 3.Xe would be Prestige Classes and feat trees.