I'm a big Roguelike fan, here's my views in order of preference
1st: Dungeon Crawl Stone Soup
I love it. it's got depth and a nice skill system, yet it's one of the simplest Roguelikes for me to get into.
it has pretty good in-game documentation, and I love the classes, they're very original, and even the more traditional classes are well-made; Barbarians are cool in Crawl, Fighters are good, Mages are really nicely made; you can be an all-rounder or focus on one school, and with a lot of customization for specialists, and the Transmuter is currently one of my favorite classes in a Roguelike. it has a wide selection of races, too. I feel all major types of roles are well-represented in this game.
also, the fights can get fairly intense really fast, which I really, really like in a Roguelike. it's just really good all-around.
it's downsides:
no Mindcrafter-type class
Spears are slightly gimped compared to some of the other weapons
Short Swords are really gimped (except for Daggers, stabbing makes up for it.)
(close) 2nd: Nethack
when you say "Roguelike," the first game I think of is Nethack. it's the classic Roguelike, in my opinion. it's got a nice and simple skill system, and some good classes. it's got really good item interaction, interesting Artifacts, noteworthy enemies, a good intrinsic ability/corpse system, interesting ranged fighting, a very classic Wizard role, food plays more of a role in Nethack than in other games, a good dungeon layout; an all-around well-made game.
I especially like the Knight class, I feel it and the conduct system is what sets Nethack apart.
downsides:
some weapon types are utterly gimped and practically useless
some artifacts are actually horrible to get because they make it harder to wish for more artifacts
I HATE how the game doesn't tell you what a weapon's damage or an armor's effectiveness is
there's not enough races and there's almost no reason to be any other race but Human (only Rangers and Wizards have any reason to be Elves) the religion system is a bit too basic to me (I love multiple deities)
the fighter classes are so similar.
I mean, sure, Crawl has 2 fighter classes that are practically clones, but in Nethack, the Barbarian, Caveman, and Valkyrie are practically the same except for artifacts and an intrinsic or two, but you can wish for artifacts and gain intrinsics.
also, I personally dislike the inclusion of the whole "Sokoban" thing; sure, it's fun, but I have to do it every time?
(despite all this, I'm a big Nethack fan, and recommend it to others.)
3rd: Iter Vehemens ad Necem
despite it's flaws, it's really fun and innovative. it uses a limb system; enemies attack your limbs and you attack theirs (randomly,) which could result in survivable things like losing an arm, or deadly beheadings. what makes it fun is that you can get new limbs made out of various materials like crystal, iron, spiders' silk, or even angels' hair.
another thing that improves the atmosphere of the game is sometimes having to resort not just to cannibalism, but the eating of your own limbs for survival. it really gives the "survive at all costs" feeling; even vomiting and laying banana peels plays a role in your tactics.
another thing that sets it apart is that the Gods and Goddesses have very unique effects, but you're not limited to just one deity. in general, it's better to stick with an alignment "range"; like Lawful ++ to Lawful, for example.
also, it has the coolest explosions in a Roguelike, in my opinion, and one of the coolest artifacts ever because it can cause said explosions. also, the Whip of Thievery is interesting. the other artifacts are cool too.
best of all, the game never becomes too easy. as you get more powerful, your enemies do too, but even moreso than in your average Roguelike.
downsides: no character classes, you're simply a slave
you can't cast spells (but in my opinion, the well-made prayer system makes up for this; a few deities have really cool, spell-like effects)
extremely hard. I'm all for difficulty in a Roguelike, but not to the point where only a VERY small handful of people have actually beat it.
the rest of these are in no particular order; they're ones I haven't really played long enough to know a lot about, but left distinct impressions.
Dwarf Fortress
pretty cool game. think Roguelike meets Sim City, in a way.
Adventure mode is the Roguelike portion of the game, and while it really lacks depth (there seems to be no magic whatsoever; no Staves, Wands, Rods, Potions, Scrolls, or spells,) it has a really interesting Wrestling system; rather than unarmed fighters being only able to punch enemies, they can get them in locks on a limb, then break that limb, or gouge out eyes, or choke the enemy.
Swords and other sharp weapons get stuck in your enemies, so you can either twist them around in the wound to cause pain, or pull it out through Wrestling. Hammers and Maces are cool because they can launch your enemy several squares away by sheer force, often making them explode in a gory scene of guts, limbs, and brains.
the other mode is more of a Sim City-like, where - you guessed it - you're helping a bunch of Dwarves build a Fortress. it's really fun, and is probably the game's main draw. I didn't play it long, but it was really nice.
downsides: all that really can be said about this game is it lacks depth, in items and abilities. it's a solid Roguelike if your favorite classes are Warrior and Monk, though.
Incursion
it's a pretty new Roguelike based on the D20 system of Dungeons and Dragons' fame. already it's showing a LOT of promise. it's not exactly like D&D, though; armor is done differently, and some classes aren't in D&D, but I think this is a good thing, because if you wanted to play D&D, you'd just play D&D, but this game has it's own unique feel.
even more unique about it, is Prestige Classes: when you reach certain requirements, you can change your class to a totally new one, like Alienist, Tattoo Mystic, or Blackguard. I've never really seen this outside of Strategy RPGs like Tactics Ogre or FF Tactics.
downsides: it's quite obviously not complete, being in alpha stage. sometimes the game will just crash for no reason, lots of skills, feats, and abilities unimplemented
pretty brutal RNG; the first level can be laughably easy or downright unfair
Fighter classes are gimped, especially heavy armor builds; even the game's developer admits it
Rogues are the most powerful class (some may like this, and I'm not completely against it, but Rogues aren't even "combat-first" classes; to me, a Heavy Armor/2-handed weapon Warrior should dish out more damage than a Rogue
can be hard for a newbie to the D20 system to get into
Ancient Domains of Mystery
this game is pretty good. it's got a random-battle system while you're in the wilderness, giving it an RPG feel. it's got lots of classes and races (fewer than Dungeon Crawl,) and some races and classes are unique to ADOM, which is good. all in all, an above-average Roguelike.
downsides: pretty hard. getting ambushed by 12+ monsters at level 1 isn't pretty
has lots of classes, but Dungeon Crawl has almost all of them and more
Necromancers are gimped for some reason
Angband
really long game, good, solid classes, big dungeon, and has a town. pretty good, pretty good.
downsides:
whips are the most powerful weapon, practically, which doesn't make sense to me
no pure Archer class
first few levels are way too easy
the levels being so large can be a bit daunting
ToME
I'm loving it so far. really LOVE the unique classes, has decent races, and a big world plus big dungeons. having lots of fun with it, and I actually made it to level 7 on my first real attempt, yet it wasn't too easy, either. quite nice. so far, I'm liking this game enough to feel it's superior to Angband.
downsides:
skill system can be very confusing for newbies
quests can also be a little bit confusing
in short: try ALL of the Roguelikes I mentioned, they all have their own unique flavors. in my opinion, there is no /best/ Roguelike; they all have their own strengths and weaknesses that make them unique.