Interesting thread I overlooked until now.
Setting and Story
Any game should have an interesting setting which gives the player character a reason for (whatever the ultimate goal of the game is). The setting should be consistent, it can have similarities to cliché settings, but should add its own flavor to these. Examples I like in this regard: Vanilla Angband (because of it's simple LoTR setting and it's deep depressing dungeons), Legerdemain (because it even has its own printed book). Examples I dislike in this regard: Nethack (too much inconsistency in monsters and items), Dungeon Crawl Stone Soup (often I forget why my character is in the dungeons at all).
Dungeons and World
I prefer non-persistant dungeons like in Angband and have the feeling that today most people disagree with this, because of some disadvantages, but it forces you to go deeper, deeper, deeper, if you don't want to explore all the paths to the exits of a level again. It's also good to have some kind of town level or even overworld in the first level. This strengthens the feeling of a consistent setting.
Dungeons should also have some things to play around with, for example oil on the ground that can be set on fire, or spider webs that can be destroyed by fire.
Monsters
Monster's should not be procedurally generated. Each kind of monster should have some speciality that distinguishes it from others, and the player should have to find ways to cope with this speciality. The preacher throws fire? Well, get fire resistant equipment, or resistance potions. There should also be some peaceful monsters and for some character classes, killing these should have a negative outcome (like no EXP). Monsters should also react on different dungeon states (e.g. getting hurt when standing inside fire).
Items
In general, items should be static, too, but identifying potions and rare and unique items should be required nevertheless, and there should be a SMALL amount of weapons with randomly chosen specials. It's good to have the possibility to combine items with other items, to create new items (such as combining bread and meat to a sandwich, or inserting a crystal into a socketed weapon). It's also good if enemies react on items thrown on them (such as getting peaceful, if food is given them), and if there are parts in the dungeons which react on items, too.
Inventory
Inventory size should be limited, because I simply like inventory micromanagement, and the decisions about item usage.
Quests
I like subquests, giving the possibility to get better equipment or money, and to get to know the setting and the story. I also like fed ex quests ("get me A from B") and simple kill quests ("kill X of type Y"), but many people don't.
Interface
As easy as possible. My ideal roguelike interface LOOKS like the interface of World of Warcraft or similar games and PLAYS like Diablo. As few keys as possible, and no huge boxes at the screen, except small status areas and an action bar. In console mode, of course, compromises have to be made. The interface should also let the player know what he can do in a given moment at the current position (not everything, but common things).