Dungeons of Dredmor is probably the best actual rogue-like game on the market; at least in the sense its most like the old games. It's pretty solid, but inventory management is kind of a pain in the dick and gets pretty tedious.
FTL is very, very good but is only really "rogue-like" in the sense it's one and done runs and procedural generation. The actual gameplay itself is more of an RTS in a lot of ways than anything else.
Rogue Legacy is kind of like Castlevania if it had permadeath and an unlock system. It's not bad, but holy hell is it ever grindy.
Enter the Gungeon is goddamn amazing in terms of gameplay, but it doesn't really have the longevity for me. The item pool is almost entirely guns, of which lots are not very good, and with the way ammo works you wind up usually wanting to play the first half of a run using your default weapon as much as possible just to conserve ammo. It puts you in a strange situation where you just found a really cool new gun, but you don't actually want to to use it for fear of running out of ammo too quickly and never finding a refill and then being stuck unable to progress on later floors.
Isaac is obviously great, even if I don't really love the direction they went with Afterbirth. Too much time spent making new, and often pointless/useless items, no real effort put in to balancing any existing items, and the new "challenging" boss fights are just bullshit gimmicks. Making your item build not do anything for a fight != difficulty, it's just stupid and counter to the entire points of the game.
Dungeon of the Endless doesn't really get mentioned often, but I personally really like it. The room control/activation system adds a neat bit a strategery to it. It scratches all the right rogue-like itches of "can I afford to extend just one more room here?", as well as having quite a few different party members you can acquire to shake things up.
