Depending on how you define "JRPG", some Falcom games definitely qualify. Xanadu Next's final dungeon alone is a masterpiece; the rest of the game has to settle for mere greatness. Most of the dungeons in Brandish games are superb as well, and Ys titles as new as Lacrimosa of Dana prove that Falcom's still got their dungeon design chops when they need them.
SMT3: Nocturne didn't have good/interesting dungeon design. It had rather small and basic dungeons with artifically-mazelike paths through them, designed to provoke large numbers of random encounters.
Which is quite frankly very standard for the genre.
Maybe that is standard, but Nocturne has some good (even great) dungeons that get around this hurdle. Kabukicho Prison, Assembly of Nihilo, at least half of the Amala Temple dungeons, and a good chunk of Amala Labyrinth have more going on than basic exploration and encounter management. The shit dungeons—mainly Yoyogi Park, Diet Building, and Ginza Underground—exist simply to waste your time rather than provide interesting things to do or see. Obelisk and the final dungeon have a potpourri mix of all the best and worst parts of Nocturne's dungeon design.
Strange Journey, meanwhile, seems rather heartlessly-built given the automap and QoL restrictions in the DS original. The 3DS remake seems to make its dungeon designs a lot more palatable simply by siding with players.
Etrian Odyssey IV has the best dungeon design of any RPG I've ever played.
It's majestic.
The first Untold already has better layouts and more FOE puzzles without slacking in pace. I think EOIV really suffers from how the dungeon content's spread out too thin across the mazes and labyrinths, coupled with simply less to explore.
Yes, Wild Arms 5 dungeons were a great mix of battles and puzzles. And I appreciated that they shut off the random battles during the puzzle parts so you don't lose you place while doing them. They even have it so you can shut off random encounters once you get far enough in so you can explore at your leisure.
Wild Arms 2 and 3 have good systems for putting off random encounters, too, though I think they needed to go even further by implementing a Bravely-style encounter rate toggle many years ahead of the competition.
Golden Sun's dungeons are still unmatched - they were huge, complex and you had a lot of different magical ways to interact with your environment. After playing the Golden Sun games I was always disappointed with the dungeon design of any other JRPG that I played after that.
Make sure to play through Lufia II and the first three Wild Arms games if you haven't already. They're all in roughly the same tier of dungeon design excellence.
As much as I love Lufia II and how the dungeons used puzzle elements in a clever way, it drove me nuts how almost all the dungeons looked exactly the same. I got to a point where I had to take a break from the game for awhile because it felt like repeating the same dungeon over and over.
I approached this game with a helpful assumption: it's a simple combat gallery and complex, exhaustive series of puzzle sets all in one. Lufia II's great because it never lets up with variations on its themes, though this definitely hurts the story a lot. Never have I met a Japanese adventure wargame as workmanlike but superbly constructed as this, for better or worse.
Land Stalker for the Sega Genesis, but honestly you will be overwhelmed.
Runner up : Alundra.
Both games are great, though the former's a lot more accessible. Alundra takes its puzzle designs to extremes that make Landstalker blush. One game's about a varied adventure while the other's about defeating nightmares however they arrive.[/QUOTE]
