You can't take it (all) with you...
For the most part, the way equipment is managed in rogue-like games is interesting, but common to most RPGs. You've got a limited number of equipment slots, and you have to pick and choose which items you want to equip in them based in their properties and your needs. In this sense, rogue-like games are fairly standard.
Where they get interesting is that rogue-like games also usually make a big deal of tracking your weight and encumbrance, causing you to not only make choices about your big ticket items like armor and weapons, but also among the smaller things. How many potions of healing are you willing to sacrifice to have room for that Wand of Fireballs? As you delve deeper, you are continuously finding tools that could be crucial to your survival, but also constantly weighing the cost of adding it to your already carefully balanced kit.
This isn't merely a matter of aesthetics, or maximizing an AC or DPS or total available healing. This approach is interesting because, often, the items themselves (and how they interact with the world) are interesting as well. There are a broad set of circumstances the player can find himself in as he descends, and thanks to the open style of gameplay each can be solved in a variety of ways. If a player has no good way of dealing with a hydra, keeping hold of a few wands of fire is probably a better idea than any number of healing potions (although the healing potions are probably going to be more broadly useful if you get into troubled). Scrolls of Teleportation are a crucial "get out of jail free" tool, but less useful for a wizard who can already cast blink. A Wand of Digging is a great way to get around problems rather than going through them -- provided that fits your character's skill set.
In general, the key is that the items act much more like pieces to a dynamic puzzle the player is attempting to solve rather than just temporary boosts. The effects are big and dramatic and let players do things they simply wouldn't be able to do otherwise (rather than simply doing standard things better). To some extent, the abilities granted by items play more like character powers that the PCs have to choose from a limited pool.
Unfortunately, rogue-likes are able to get away with this largely because they are computer-based, and so can keep track of weight very easily. On the tabletop, encumbrance rules are usually the very first thing to get chucked out the window (either intentionally or through laziness) because it's just too much work to keep track of. Still, there are things a DM can do to encourage a similar type of aspect to their games. One option is to present players with a choice of rewards (Wonderous Items or Boons work great here) but only allow them to select a single one. Another would be to present players with a set of interesting items to buy, but keep cost as a limiting factor so they have to choose what they take with them because they can't afford it rather than because they can't carry it all. Of course, if you can find a way to make tracking inventory manageable then you've got a whole array of interesting emergent options out there. Your players will almost certainly end up kicking themselves at SOME point for leaving their 10-foot pole or door spikes at the inn so they could carry that extra Potion.
You delve with the loot you've got, not the loot you want
The other key element about equipment in rogue-likes is that it is (for the most part) completely random. You may find a worthless rusty orcish axe inside a locked chest, or a suit of crystal plate mail on the first level. However, the rub is that as often as not these items are not immediately useful to you. What do you do when your wizard finds the plate mail? What if he's about to descend into the toxic swamp, and it's the only source of poison resistance he's found so far?
The key to random generation is that with enough time the player will discover the things that seem useful to the "ideal" of his character; however, at any given time he is likely to never have exactly what he or she is looking for, and so has to adapt his strategy somewhat. In the above example, the wizard simply doesn't have the skill to make wearing the plate-mail worthwhile; if it was a chain mail shirt with poison resistance, though, he might have to consider whether the added difficulty for casting spells is worth the extra survivability (at least for the near term). By throwing in useful but not ideal items, you present the player with interesting choices that can serve to validate otherwise suboptimal character builds (like a wizard with armor training or high strength, or a fighter with above average dexterity). The randomness does not necessarily remove the "system mastery" aspect of character development, but it does provide an incentive for adaptation and flexibility which moves more of the interesting decisions away from the pre-game stage of designing a build and back to the moment-to-moment decisions at the game table.
In this spirit, I try and make sure at least some portion of the loot I hand out is random (and rarely do I try to target it at a specific character). I don't necessarily select from the entire set of possible items -- usually I keep a running list of things which strike me as "interesting" rather than just powerful or good for a specific build, and will select randomly from that list. I like giving my players quirky tools to play with and watching them try to figure out how they work together rather than just giving them a +1 along the character track they decided upon a dozen sessions ago when the campaign began.