I find that my forts always get covered in blood, guts, and other nasty stuff. This usually causes lag to creep up, and eventually can kill my fort. To stop this I use hacks to clean things, but perhaps a different solution could be put into play.
The waste drainThis is a new designation: the waste drain. Basically, its a place where dwarfs dump contaminated water after cleaning. The player can decide to make it a cistern that will eventually fill up, or the player can make a pipe system that allows it to drain out of the map. The player could even use a dwarfen atom smasher, or come up with some other ingenious or purposefully stupid system of waste disposal.
Mopdwarfshttps://www.youtube.com/watch?v=PaoU3_u-c_gA new labor: mopping. A dwarf that has mopping has his highest skill receives the class "mopdwarf". Instead of mopping randomly, mopping would work like mining, allowing the player to select the areas they want cleaned. And instead of being armed with a pickaxe, mopdwarfs need a mop and a bucket. Mops are made out of wood or metal, and require a "mop head" made out of some form of cloth. Sheep wool works the best, and can absorb the most waste before it needs to be cleaned in a bucket. As for the bucket, its an item already in the game. In order to mop, a mopdwarf first has to fill his bucket at a water source. After cleaning a few tiles, the dwarf's water bucket gets contaminated. After this, the dwarf has to empty the bucket at a designated waste drain, and then can refill the bucket to repeat the process.
The soap-mixerIf a player wants to spend more resources to create a more effective cleanliness industry, the player can create a workstation called "Sopamixing". When mop dwarfs are not busy cleaning, they gather soap and water in the workstation, and mix it together to create "soapy water". While mopping, mopdwarfs can fill their buckets with this water instead in order to mop more effectively.
The Plague SuitSometimes, substances that the player encounters in dwarf fortress can be incredibly dangerous to dwarfs, causing nasty effects like necrosis. In order to help dwarfs to be less defenseless against these contaminants, I recommend a new clothing type: The Plague Suit. Made of leather, a dwarf wearing a full plague suit is completely protected from contaminants. However, dwarfs can still breathe in contaminants, unless they filter the nose-piece by filling it with golden salve. Over time, this salve needs to be replaced in order for its effectiveness to be maintained. This cloathing can be assigned to doctors, mopdwarfs, and even military dwarfs. There could even be a metal variant that provides a bit more protection in combat situations.
The washroomEven in ancient times, people took a bath. Some cultures did it only occasionally, while others did it every day. Bathing would be a wonderful addition to any fort, because otherwise it is almost impossible to clean dwarfs after they get dirty. I propose the washtub: a new workstation. Washtubs can be made out of wood, stone, and metal. Also, I propose the bathdwarf, a new class of dwarf that's highest skill is bath management. It is the bath dwarf's job to maintain the baths in the fort, changing their water. Taking a cold bath can give dwarfs unhappy thoughts, so warming the water first in a water-heater workstation can be smart. Dwarfs can be set to take baths automatically when they get dirty, and also the player can select individual dwarfs to take a bath as soon as they can in the workstation's menu.
Of course, more options for the player to choose for cleaning would be great. One idea is a special drain, that when water goes through it to the z level bellow, it creates a "shower", which freely passes through drains without building up, and will only build up as water again when it hits a solid tile. There could also be a way to designate water pools as a washing area, and there could be a water furnace designed to warm up water tiles adjacent to it for this.
The QuarantineIf things get terrible in a fort due to some nasty substance, or a disease (if these are ever added), the player could have the option to designate an area of their fort as a quarantine area. Military dwarfs can then be assinged to different areas to help enforce this quarantine. Of course, there is always the opportunity for the infected dwarfs and their loved ones on the outside to get mad about their separation and start a riot, most likely with devastating results.
If things get super bad, a player might order bodies to be burned. This is effective at stopping a contamination from spreading, but it also creates unhappy thoughts because of "the smell of burnt flesh", "loved one was cremated and didn't receive a proper burial", etc.