There's actually quite a few more modern roguelikes out there, mainly because the genre is
extremely popular in Japan (they're called "Mystery Dungeon" games). Some of them, particularly the Fushigi no Dungeon series (made by a company called Chunsoft, who had developed the earlier Dragon Quest/Dragon Warrior titles), are
extremely well-made and fun. Not many of them ever make it outside of Japan, but a few have, with the most popular ones being the Pokemon Mystery Dungeon games (yeah, those are roguelikes).
If you live in North America and have a DS, you could also check out Shiren the Wanderer, which was recently released for it. Not
strictly "modern", since it's a port of a Japanese SNES game, but it is a recent commercial roguelike release, but it's still worth checking out, as it's an
extremely good game (quite possibly my favorite roguelike of all time). There's also Izuna: Legend of the Unemployed Ninja for the same platform, as well as its upcoming sequel, but I can't say much about those ones because I haven't played them.
Now, if you're looking specifically for 3D ones... well, slim pickings there. There's Nightmare of Druaga on the PS2, released in 2004, which is good enough and has a few interesting mechanics (rather than eating, you sacrifice items to power your magical armor, which also determines your light radius). There's also Chocobo's Dungeon coming out in July, assuming you don't mind a massive overdose of both Final Fantasy and adorableness.
Shiren the Wanderer 3 looks very nice, both visually and otherwise, but... well, no confirmed localization yet, and it's a Wii exclusive. There's always a chance that Sega will localize it for English-speaking regions like they did with Shiren the Wanderer, or that Atlus'll be interested in bringing it over, but it's not particularly likely.
