Applying some realism can always be a limit.
If need be, build in a semi-realistic fashion with buildings or other projects (EX: Bloodfist's development; make skeleton and infrastructure before developing the rest of the structure. As well, work floor-by-floor).
If we want to apply this limit to more extremes, scaffolding is a necessity for large structures, but cannot be exclusively stairs everywhere (too easy), but are ramps and floors (more what scaffolding really looks like).
Distillation Plant: All water must be distilled first. IE- Treat all water as if were salinated or has potential for infection, even if not. Let's not risk our citizens' health just because the water was "just there". Especially relevant in haunted/evil/terrifying biomes. If possible, boil the water first, instead of using desalination pumps.
Stone quarries must be handled like quarries should be handled. Find pictures for reference.
Selective Harvesting (of trees): Especially if having a wood economy (lots of wooden structures or objects/items/buildings), preserve the environment in aesthetic, and income. Be selective with what trees you collect. Elvish it sounds, this can be a great help for island embarks. Especially if you can't collect stone due to aquifers.
Building Permits: Structures must follow a building code.
Guilds: Make use of those burrows to form guilds.
Sewers: All towns or large fortresses must have some sort of plumbing with flowing water. Pumps may or may not be required.
Aqueduct: Similar to sewers, embark a distance away from a water source (river/brook/aquifer), and make an aqueduct.
-If you want, do similar with magma instead.
...Why do I sense that I might make another list of sorts?
Here's another (set of ideas):
Migrant Gauntlet: Make an alternating spike-strip repeater system (3x3 may work; can double as an anti-ambush/siege system as well.) for the entryway of your fortress. Of course, this only applies to new migrants, nobody else. (2 migrant burrows may be required. MigrantA and MigrantB. A=Gauntlet start, B=Gauntlet end.) Sort out the remaining migrants for their tasks. Lost someone potentially useful? Too bad. Alternatively, you can make an obstacle course for them; let's hope they survive it. You can deal with the migrant wave now, or stockpile migrants and feed them until you decide to overwhelm the gauntlet.
Warrior Proving Grounds: Similar to Migrant Gauntlet, but this is an annual test for all your warriors. The elite have to cross the migrant gauntlet as well in their test. Lost a really useful trooper? Too bad. Tantrum Spiral occur due to thick bonds between warrior and etc.? Have fun.
Capitalism Ho!: Start your economy as early as possible, and work deal with it.
Nobles, but No Bliss: You cannot commit regicide with any noble unit, no matter how much you hate them.
Carbon-Copy: Design your towns/fortresses in a similar manner to what you see in Adventure Mode (Old and New). Includes ill-planned bridges, huge farmlands, and hamlets and etc.
This Isn't Minecraft!: With only 1 dwarf, establish a settlement and survive. They'll be equipped with all the necessities and be assigned all tasks. Pre-Requisite: Terrifying biome (skeletal creatures and zombies abound. GCS is a bonus). Further bonus if it converts well into MC with the DF-to-MC converter.
More Elaborate City Infrastructure: Structures that can, and probably must be created in your town/city: Immigration office, Courthouse (complete with courtroom), Police station, Hospital/clinic, market/supermarket (all structures must be built to code).
Tourism Industry: Especially if you have a scenic view, or an island embark; make use of burrows and construct a tourism industry, and see if you can integrate tourists into becoming citizens of your town/city/fortress. (economy required)
Anthill SimAnt: Not all stone can be used for manufacturing. For every 5 stones found, 1 must be constructed atop an access point as a wall/ramp from the access point to underground. Look at ant colony structures for reference. (Prerequisites for additional challenge: GCS is a must. No stairways, only ramps.) (CAUTION: To ease up on the size of the hills, make multiple openings. It may compromise security however.) (Bonus points if: You can force castes via burrows (Breeders, workers, and warriors))... You know what? Let's just rename this limit/challenge to SimAnt.
SimTower: In the same vein of the above challenge/limit, we're essentially making a DF conversion of a classic. In this challenge, the prerequisite is that you must be working with the "Capitalism Ho!" limit; so early economy is a must. If you've played SimTower before, you know what to do and expect. If you haven't, just try the game out before you attempt to replicate it (and for a unique challenge: go for 100 floors, and also follow the star prerequisites as featured in-game). It's like the tower challenge, but you must have a working economy to build a tower upwards and onwards. Have fun with this one. At least you have the benefit of working on this in a 3-dimensional space/scale. Scoring is based on the value of the building. Obsidian-casting is allowed. Figure out how to make an elevator system (which BTW is a 30-floor limit, so place wisely). Lobbies cannot have anything inside (or at least, Floor 1 cannot have anything inside). Build them every 15 floors. Speaking of which, express elevators only go to other lobby floors (and can individually reach underground floors as well), and has no height limits. To make this one aggravatingly more challenging: Build it to code. Add cubicles as well if you must if it's an office. Restaurants/pubs must be built like restaurants/pubs. Security offices = Barracks. Oh, and with the Star requirements, 1 Dwarf = 100 people; for FPS reasons.