I couldn't find much suggested about this when I searched, so here goes;
With the advent of the Z-axis, making water systems is going to be a lot easier.
My suggestion is to include a buildable 'privy' that dwarves will use, and deposit detritus onto an empty space on the level below. Obviously this will cause miasma given time, so a refuse hauling dwarf would need to move it outside or dump it in the chasm or river.
Enterprising players would probably use running water to safely flush the detritus away, and that would make things a little more interesting by giving amphibious enemies a way to infiltrate your fortress, so sewer guards or filtering systems would be needed.
Some other related ideas;
- A more interesting role for vermin - rats could feed on refuse and food. Sewers then could make rats a major problem. This would make cats more useful, or give the player the opportunity to assign dwarves to full time rat-catching duties (trappers).
- Sewage could make water dirty. Obviously, you don't want your dwarves drinking dirty water.
- Sewage could be used as fertiliser for fields (giving bad thoughts to the unfortunate manure-shovelling dwarves) or could be left to compost, which would do the same but without the bad thoughts.
What does everyone think? It would cause a bit more micro-management, but that's what the game's all about. It would also give more uses to features that are already in the game. (Vermin, Cats, Trappers, Guards, Refuse haulers and Miasma.)