This wouldn't work in some earlier Dragon Quest games:
* DQ2 and DQ6 have mandatory items sold in shops. (Well, in DQ2 you *could* get around this by leveling up high enough, but that wouldn't be much fun, and would make the later game easier than it would be if you hadn't don this.)
* DQ3 has one item in a shop that you need unless you raise a certain class to a certain high level and learn the spell that mimics the item, and the level it's learned at is of course somewhat randomized.
* DQ4 doesn't have any mandatory shop purchases IIRC, but I think Chapter 3 would not be much fun without the ability to use the shops. (Worth noting that Chapter 3 in DQ4 has random wandering shopkeeper encounters, a mechanic I've only otherwise seen in Demon's Winter.)
Shin Megami Tensei: Nocturne does this on its hard difficulty setting.
mqstout: Strategy games often have lots of places to tweak, too.
Civ4 has a whole host of them at the game creation screen (and even more if you look into the config files to create your own custom difficulty level.
Old World does too.
Of course, it's possible to create configurations that don't lead to meaingful gameplay. Like, in Civilization 3 for example:
* Solo play with no other civilizations, with Conquest Victory enabled; you win right away. (Note that disabling Conquest Victory does not disable Conquest Defeat, as there's no other sensible way for the game to handle the player's civilization being wiped out.)
* Degenerate custom maps. A map of all mountains is an easy victory, as the opponents will all disband their settlers (I assume their AI panicked looking for a place to build a city), while a map of all water will cause the game to fail to start, with an error to the effect of "can't place initial settlers".
Engerek01: A long time ago I played an RPG and increasing the difficulty didn't seem to change anything... at first. Then I realized it made the enemies "smarter". Common thugs were still the same but enemy Ninjas hid in the shadows and backstabbed my healers or wizards instead of blindly sharing at my tanks. Archers shot me and then ran back, pulling me into traps. I was really impressed.
I've heard Shining Force 2 does something like this. The two middle difficulty settings increase enemy stats, but the hardest puts the enemies at their default stats, instead upgrading the enemy AI.
mqstout: The worst: Time limits. They're awful game play. There are some turn-based games that have time limits applied to your selection and difficulty settings reduces that. Unfathomably stupid.
I think time limits could work in a special time attack challenge mode, or perhaps in a game that's meant to be a racing game. (A time limit on a race would be better than a rubberbanding AI; in the Goron race in Zelda: Majora's Mask, I'm pretty sure my personal best time was a loss, even though I have managed to win.)
Braggadar: - Don't punish lower difficulty players with locked content (difficulty should be rewarded with the satisfaction of meeting the challenge, not giving the user more content).
*shakes fist at Castlevania 64, which ends early if you play it on Easy, and the game and manual give you no warning about this*