I'm a huge fan of the Shiren series. The latest one is really good. Really they're all good, but many of the previous ones weren't localized so you'll have to rely on fan translations. The Torneko and Chocobo Mystery Dungeon games are also solid, especially if you're a DQ/FF fan.
If you're looking for something less difficult, there's Izuna the Unemployed Ninja and its sequel, which isn't officially a Mystery Dungeon game but plays pretty much the same. Tangledeep on PC as well.
Getting into more obscure territory there's The Nightmare of Druaga on PS2, which is an official Mystery Dungeon game despite lacking the randomized element. Other games that aren't MD but are good and play similar are Azure Dreams, Cave Noire, and Dragon Crystal. If you want to play the MMO version of a Mystery Dungeon game, there's Elona/Elin. There are also a lot of Japan-only games in this vein, like Shiren Gaiden, Shounen Yangus, and Waku Puyo Puyo Dungeon, which sadly haven't been fan translated.