One thing that I don't think this group has is a thread for folks to drop their ideas for interesting historical events. That way other members could borrow them or help elaborate on some of them. Anything that drew a lot of interest could get it's own thread.

I'll go first with a few of mine, some short and some longer, and we'll see if anyone else is interested.

Wars

The Aquastrian Civil War, not technically an Equestrian conflict but notable for the highest amount of casualties suffered by Equestrian troops in a single battle - not due to any enemy action, but rather the fault of inadequately cast water-breathing spells.

Equestria's most recent (pre-show) military conflict, the Intervention in Saddle Arabia. (To give some perspective, at least two of Twilight Sparkle's as-yet-unmarried grandparents fought in this one.) Long story short, it also started as a civil war between various contenders for the throne, but when Princess Celestia issued her standard call for them to stand down and try to settle their differences peacefully, only the local Celestian Church did so - and were promptly slaughtered by both their enemies and their former allies.

Now Celestia has a rather awkward relationship with those sects, but she could not in good conscience let them be slaughtered just for obeying words she hadn't really expected anypony to heed. She came before Parliament with her crown off and begged them for an army, and they gave her one. The war was short, but the mopping-up long, and an Equestrian garrison remains stationed in the country to this day - many other countries consider it a puppet state.

(No, I'm definitely not channelling some frustrating modern conflicts through a lens of Ponies Can Do Better, no siree... )

Plagues

The Fractal Fever did much to finish the job King Sombra started - some at the time even believed it his work, although much older records of the disease were found in the restored Imperial Library. An affected crystal pony's negative feelings become literal toxins, and their pain manifests as jagged, crack-like patterns on their coat. The only known cure is the light of the Crystal Heart, and so most pureblooded descendants (including the last Far Northern enclaves) were wiped out, leaving only those sufficiently hybridised to resist the illness.

Transitions and Changes

Abolition of Slavery*, a cause which Princess Celestia had been quietly backing for some time before it actually occured - the collapse of the continent's foremost slave-trading nation gave her hope ... until it became clear that Equestria was now the largest center of the trade by default, and she realised that she would have to force the issue.

*Of non-ponies; ponies enslaving each other had gone out with the Founding and had never been tolerated under Celestia's reign.

So she gave a speech explaing how seeing their neghbour rot to death from within had convinced her that the corrupt institution was an affront to Harmony, and she summoned ponies (and a few non-ponies, freeborn and former slaves) from all over Equestria to a Great Summit that would seek a better way. The debates were contentious, but eventually the delegates settled on a complicated successor system, decried by some as undermining the very fabric of Equestria and others as merely perpetuating slavery under a new name. The Princess then signed it into law, and transition took place over the next decade without any part of Equestria collapsing economically or rising in rebellion. (The events in Mustangia which necessitated the Reconstruction were decades later and only loosely related, so they don't count.)

The Republic of Manehattan can't exactly be called an event, seeing as it lasted nearly two and a half centuries from it's peaceful secession to it's equally peaceful reintegration into the Realm. (The Pony of Liberty was a centennial gift from Princess Celestia.) Rightly or wrongly, it's often held up as an example of either the potential or the futility of of a democratic pony state.

So if anyone wants to elaborate on these, or post their own...

6742512
The Second Griffon War. I am calling it the second because my history has established a first one prior to the founding of Equestria. So, under their famous first king Grover, how did the griffons achieve prosperity. Easy, they attempted to conquer Equestria for its wealth of gemstones¹
and fertile farmland.
The griffons, attacking in an unstable period after Luna's banishment, conquered eastern Equestria and besieged Canterlot, capturing princess Celestia. They were eventually removed from the country by a rebellion of ponies after twenty years.

¹ This fact is evidenced by about five sixths of the Rarity episodes in the show

Well that's a great topic! I think it may be very helpfull to me.
I don't read much about already written Ideas (rather lack of time now... and sorry for my english, if anything isn't clear just ask - though I'm not sure if I'll be able to reply quickly) but I thought I write shortly about some of my ideas with short explanation. (Later Maybe I'll ad some more details)

Alchemic War
based on following assumptions:
- magic is actually rare in Equestria(in regard of species), Ponies are one of just a few magical races and are most magical giftewd of all of them - making Equestria one of the most powerfull countries in the world
- Zebras are masters of alchemy, which can rival even unicorn magic, making them also one of most powerful countries in the world
- Zebras cautiosly guards secrets of alchemy
So... as You could guess - it's a war that was meant to possess secrets of Zebras Alchemy. Their secret was defended, and war resulted in current zebras isolation (what was one of the reasons ponies knowledge about them is so bad)

Gunpowder war
based on following assumptions:
- As we can see there are fireworks in Equestria...
- ...but theres no firearm!
So... why? Here's my Idea. Gunpowder was designed in one small kingdom, ally of Equestria and used for such things like fireworks. Though some coutries saw military potential in it. Then one of them start a war in order to steal secrets of gunpowder production. Initially they succeded, but eventually, when Equestria join the war they lost. The damages in that war were enormous, so treaty ending the war banned military use of gunpowder at all. The other countries signed such document shorlty after, and with most powerful countries as guarantor of this treaty no one actually dare to break it. So we don't have firearms (or even gunpowder cannons - I'm not saying about such things as party cannons).
(This was actually inspired by one chapter of "Love Tap of Marendelle" - which BTW generally nicely expand history of the universe it's part of - I mean Royal Canterlot Family).

Dragon Storm
An great invasion of dragons, stopped by Equestria and it's allies. I think the idea it's self-explanatory, considering how most of Dragons were depicted. Ended by killing current Dragon Lord (maybe... that one from Smolder story in season 8?) - in my universe he was killed by Prince Aurus (alicorn, predecessor of Celestia and Luna - but he was NOT their father)

Great Pony-Changeling war
...which was the reason changelings were thought to be extinct. At that war previous changeling queen was killed and most of the changeling - which were the first to attack, and were relentless so Equestria hasn't other choice actually - were wiped out...
But young queen Chrysalis with some changelings survived and then rebuilding the hive.
(That would be good explanation why nopony even expected nothing about changelings... and yet Cadance knew exactly what they are...)

If anyone is interested can also look at this topic, about my universe. Some ideas used in it can apply to other universes too.

(And when I will have more time I will surely analyze other ideas posted here)

I always assumed that at some point in fairly recent history, although probably not at the same time, the griffons and dragons (under a particularly ambitious and organized Dragonlord) each decided to invade Yakyakistan. In both cases they bogged down in the freezing conditions and were forced to make embarrassing and costly retreats; the fact that their empires fell apart not long after is generally not considered to be coincidence.

Interesting. Why did Equestria intervene in Aquastria?

6969734
Old treaty of friendship between the Sisters and King Leo - he helped them on their quest for a way to defeat Discord. Plus, the two countries had a fair bit of trade.

Luna suffered three betrayals before her descent into Nightmare Moon[1]:

First was being seduced and then betrayed by her lover, who specifically did it in such a spectacular and gruesome fashion as he was secretly a master of a magic that drew upon hatred and the oh so personal hatred of a demi-goddess was all the more potent. She hunted him down and ultimately killed him by removing safeties in his magic that prevented the poison of hatred from killing him.

Before this, Luna had allowed her sister to screen potential consorts as Celestia was that much better at reading ponies. However, Celestia oft used that position to try to convince Luna to take consorts for political purposes, until Luna got fed up with the meddling and stopped taking her sister's advice. After that, the hate wizard happened and a divide grew between the sisters, as well as Luna not taking any more consorts, becoming increasingly more lonely and isolated.

Next, a merchant prince sought to gain control of Equestria by taking its economy hostage. Luna tried to combat him, first through laws and then military intervention, becoming increasingly heavy hoofed. At every step, the sisters disagreed how to approach the problem and their discord allowed the prince to gain further control and drove Luna to increasingly drastic measures. That and the economic turmoil threatened to mire the country in rebellion and Celestia was forced to censure her sister and force her to step down.

Last, years later, Luna took on an apprentice and aided her into becoming an alicorn. Filled with sentiment against the nobility and the bourgeoisie, Luna's apprentice used her newfound status to push for radical reforms and was assassinated. Luna went nuts, began a violent purge and pushed for her dead apprentice's reforms even harder. Once more, Celestia was forced to intervene and backed by popular approval sent Luna on sabbatical, a temporary exile until the whole thing blew over.

Luna used the time to seek out the power necessary to rule unchallenged and make herself queen of Equestria.

[1]Each of these based on a different fanfic where something similar happened, but rather more to Celestia or Twilight.