Originally I was thinking of an idea for a mod where one could play as a verminous civilization that uses hives in another civilization's site to feed off of their crafts and whatnot. However, I don't think this is possible as a mod.
That got me thinking about vermin and how they could cause problems, both big and small, for a fortress. Recently another user
posted about clothes moths and how they could cause problems in stockpiles, and I think that's a great start. Another vermin that would be interesting to have are termites, which would have a similar effect on wooden furniture and maybe even trees. I think there's already plans for that if I'm not mistaken, though. These vermin would degrade item quality slowly over time before the item disappears altogether.
What I'm really interested in is the idea that vermin could start hives within your fortress and cause issues. For example, wasps (or yellow jackets or hornets) that steal supplies like wood or paper to build a nest and then terrorize your dwarves thereafter. Fire ants would also provide an interesting terrestrial equivalent.
Or how about rats/mice that are able to turn walls into mouse holes that connect all over the fortress, stealing food and spreading disease? Parasitic vermin are also an option that could produce a lot of fun.
Circling back around to my original mod idea, I think it would be interesting to give fairies, pixies or some equivalent their own civilizations. While they may have some independent giant hive sites on the map and send out caravans, they might also form hives on your site and steal goods for their own purposes. It would be a twist on the idea of having squatters show up by your fortress and form their own homes, because the fairies might actually be able to form homes
inside of your fortress and cause issues. The hives could work similarly to normal bee hives, or they might be more like the mouse hole idea I proposed where they sort of teleport vermin to where they need to go. The fairies could go to war with your civilization, and use dwarf-sized weaponry as siege weapons or simply swarm and sting/bite dwarves.
This could give rise to a new Exterminator job who tries to eradicate vermin more effectively than a cat or other verminator pet would. The Exterminator could also capture vermin and put them in terrariums/aquariums for decoration.
Toady recently mentioned dimensions in the Future of the Fortress; because fairies are often associated with mirror worlds or hidden worlds their home sites could be located on some other plane of existence. Or the game could process their hives and other vermin hives as pocket dimensions to represent the difference in scale. Maybe a dwarf or an adventurer could somehow shrink down and enter an invasive hive. Combining this with the idea of parasitic vermin, your dwarf's very body could be entered by an exterminator to take care of a nasty tapeworm.
Perhaps the fairies are a larval form for the larger and more dangerous fair folk, who might not be so kind when their broods have been smashed open by the dwarves and send invasions, whether through other worlds or your own. When a fairy grows to full size it would be kobold- or gremlin-like in terms of behavior, causing mischief in your fortress, but on a much larger and more lethal scale.