Observations from a long-term (56 year) fort:
The fort in question, Ringlabor, is in 44.12, so some of these may no longer apply, but I wouldn't be surprised if most of them do as they are things that only come up after long-term play.
*Encumbrance: With most dwarves in a militia and uniforms set to replace clothes, most individuals are carrying few things. The exceptions are miners, woodcutters, and a few others that I've kept out of service due to their skills. After nearly 60 years they are loaded down with page upon page of crowns, bracelets, amulets, earrings, rings, etc., and take forever to get anywhere.
*Historical figures: Historical figures of mortal races are dying out. All of the visitors are old; new performers, scholars and hunters are not being generated, so if I keep this up eventually I'll have no visitors except for the occasional troupe that includes elves and goblins. (This may also be reflected in the lack of offensive action elsewhere in the world: the leaders have died off. I'm puzzled by the occasional attacks I see on the map on sites I know are empty; why haven't they been taken over?)
*Geriatric human mercenaries: I wish there was some way to gracefully release mercenaries from service, or that human aging was a bit more realistic. Currently there are 13 humans at Ringlabor, all between the ages of 75 and 114 (every new year I expect half of them to die, but they're still kicking). It'd be kind of nice to let them go home to their families, or at least recognize that 114-year-old archers are probably going to be more of a problem than a solution no matter how awesome their stats are (and with decades of doing nothing but training, these are some killer centenarians). (Or maybe these guys think of Ringlabor as an awesome retirement community.)
*Professions liable to anger and frustration: I take an "activist god" role with things like remove-stress, and have been recording who needs it for 15 years. The individuals with the greatest propensity to get red arrows are scholars and marksdwarves. In the former case, it's because they refuse to do anything else but scholarly work (one of the favorite topics is the retort, which I know is a vessel for distillation, but it's funnier to imagine them working on snappy comebacks instead). In the latter, I think it might have to do with marksdwarves being confined to sealed bunkers during combat, so they don't get any benefits of physical combat.
*The curse of the traveling scholar: The propensity for anger also extends to visiting scholars. After decades of wandering from place to place, they've gotten cranky. Several have gotten into fights over the years, resulting in visits from the friendly guard squad. These visits are brief and emphatic.
*The curse of the traveling scholar, part II: Apparently visiting scholars and performers are recruited to serve when a site is under attack. With the dwindling number of historical figures, a site's defense may be nothing but scholars and performers. I have discovered that in several cases squads from Ringlabor, tasked to raze a forest retreat or dark pit, have killed a string of historical figures that turned out to be visiting troupes and scholars (sometimes scholars who have visited Ringlabor numerous times). Oops.
*Putting on different hats: Conquest of other sites has led the Duke to decide he's duke of these other places, not Ringlabor. (He still demands production of battle axes every so often, so his head's in the right place.) Meanwhile, a couple of times a human performer has been elevated to a lord of somewhere else, but functions more or less the same except for apparently being treated as a squad in their own right if a militia member. I've had to manually add them back when this happens. There probably should be a function such that individuals who become nobles while at a site are recalled to wherever they're supposed to be ruling (or maybe for RP purposes they were named nobles because the people who elevated them knew they weren't coming back).
*Rules for raids:
1) Copy save before beginning a raid, just in case
2) No production of weapons or armor occurs while squads are offsite, to avoid equipment issues
3) Squads are stationed and then unstationed before they are sent so they aren't carrying anything
4) Squads that go offsite always have armor set to replace clothing
5) Never save a game and quit while a squad is offsite
I don't know if any of these help, but I've never had a crash. The tedious bit after a raid is reassigning cemetery space (I just let them pick their own bedrooms again).
*How to make monster hunters apply for citizenship: I have tried this twice successfully:
1) Accept petition from monster hunter
2) Send monster hunter to another holding
3) Eventually monster hunter returns, under a different profession
4) Monster hunter will now apply for citizenship two years after return