I like the simple approach where you directly get money from enemies, rather than getting items that you have to sell for money. Makes inventory management a lot simpler, and means less work when you do finally get to the store.

One interesting system I overlooked happens in False Skies, once you get to the later part of the game. At this point, a new currency is introduced, that has something like different denominations of bills, except that you can't convert between them. As a result, buying cheap consumables and restoring your party doesn't affect how much high-end equipment you can buy, and vice versa. I think it's a rather interesting system. It may not make sense, but it's simple to implement, and has lower cognitive load on the player than the other alternatives, and there's something to be said for that. What about a system where enemies always give money, and you can use the money either for items or for powering up your characters?

SaGa 1 does this, at least if you're using humans. SaGa 3 (original, not remake) does this for robots.

I think I may have seen this sort of mechanic in some non-RPGs as well. Maybe Romance of the Three Kingdoms (NES)? And I remember a sports game where you could improve a player, but it had the side effect of increasing their salary. (Incidentally, Might & Magic 2 is an RPG that does something like that; if you level up a mercenary, their daily cost increases, though you don't have to pay an upfront training cost as you would with player-created characters.) Every now and then, there's an RPG that actually lets you do this, like the aforementioned SaGa 1 and 3 (though, in SaGa 1, it gets to the point where spending the money on stat boosts takes far more time than earning the money in the first place). I think some FIre Emblem games let you do this, and although it isn't an RPG (by my definition), Ys 6 allows you to buy HP increasing seeds late game.

Also, Avernum 1 and 2 have a shop somewhere that sells an item that permanently grants skill points. If you buy out the entire shop (expensive!), the shop will restock, complete with more of that item. (Note: This doesn't apply to the later remakes, but may apply to Exile 1 and 2. Also, Avernum 3 instead gives you a recipe for creating that item, though that recipe is treated as a major artifact, making it as hard to get as certain endgame pieces of equipment.)