Crawl, Incursion, ToME4 and The Slimy Lichmummy use multiple items per tile, off the top of my head.
Crawls tile mode handles it deftly since you only need to hover over the pile with your mouse in order to have the contents displayed on the right hand side of the screen.
Incursion opens its item handling menu when you pick something up (allowing you to take an item from the floor into your hands, and then to one of your equipment slots or into a container). Alternatively you can look at the tile to see a list of the items there. Optionally you can have the game display all items in view in one of the sidepanels, which is VERY nice.
ToME4 (which uses tiles) displays one item of the pile as a graphical tile and adds an asterix to denote that there's other items there too if memory serves. Picking something up opens a menu that lets you pick the items up one by one (or all at once).
Slimy Lichmummy simply has multiple items per tile and says it's a pile of stuff. Opting to pick something up gives a simple menu akin to Nethack. That's in SDL mode, I don't know how ascii mode does it, since I prefer the SDL mode, derp.
Of these three types of handling (ToME and TSL are practically the same) multiple items per tile, Incursion does it best for pure Ascii in my opinion. For tile-based roguelikes there are a lot of lessons to be learned from Crawl's interface, which is brilliant in conveying information.
Both of these have the ability to have the game display items in a seperate panel, which is crucial.
Crawl's tile mode is (to me) unplayable in that seeing what's in an item pile is so damn unintuitive and timerobbing.
The more often you have items in a pile, the more crucial it is to have a way to display them at a glance, and sidepanels (or Angband style seperate windows) is more or less the only way to do it in Ascii.
Crawl and Incursion have LOTS of item piles though. The Slimy Lichmummy , Nethack and ToME get away with the Nethack style pickup menus because they usually have only single items lying about.
Personally I prefer roguelikes to be smaller in scope and tactical (NETPACK, Slimy Lichmummy, Forays into Norrendrin, Sword in Hand and PrincessRL as examples), which has them be more conservative with their item drops.
More piles usually coincides with games having lots of equipment slots. Sure it's fun to deck out your @ with boots, pants, underpants, belt, belt buckle, undershirt, t-shirt, vest, blazer, gauntlet, ETCETCETCETC but that leads to either an Angband-style roguelike (which is opposite to my preference and therefore objectively bad
) and/or a lot of the items being garbage/useless/squelchable.
Comes down to me preferring single item per tile; I'm a big fan of removing obsolete elements from games, like having a single button fill multiple roles ('a'pplying a potion, rune, wand, magic ring ability etc). More towards pong, less towards Dwarf Fortress, you know? But that's a whole nother topic, sorry.
Having a single item per tile also means developers can simplify their UIs.
In the end it depends on the flow of your game, how tight your design is and what role items play in it.
Add.: I can't remember if it was Halls of Mist or Sil that did this, but they had single item per tile, with items rolling to adjacent tiles. That's a fine way of handling multiple drops, BUT.
If you have DOORS. For the love of god please don't have the door be BLOCKED (making me unable to close it) because a scroll or an apple rolled onto the same tile.