Not sure if it will count, but the Ancient Cave in Lufia 2 (SNES) was a game in and of itself. It was basically a roguelike dungeon. 100 random floors, it reverts you to level 1 and there were rare special items you could sometimes find in runs that could be brought back in. Beating the Ancient Cave is much, much harder and more rewarding than beating the game itself (storyline aside).
I thought of another one. There is a minigame in Xenoblade Chronicles 2 called Tiger! Tiger that is great. it is basically an arcade game where getting certain scores gives you credits that can be redeemed for upgrades for some characters. The minigame is randomized and has three different difficulty tiers and is overall really well done.