After Doomsday. After capturing the male human protagonists, a Kandemirian officer tries to persuade them it would be best to accept their rule, as their spacefaring empire is like this and would allow the human refugees to maintain their own culture and beliefs.
A Memory Called Empire: While the Teixcalaanli Empire is still a militarily expansionist power that annexes lesser nations by force, far more importantly it's the currently dominant cultural centre of humanity. Teixcalaan language, culture and trade goods has been exported from the heart of the empire to its neighbours and rivals, to the extent that it ultimately colonizes and dominates people without firing a shot. Mahit, the protagonist, is a massive Fangirl of Teixcalaan culture and knows almost as much, if not more, about Teixcalaan protocol than the culture of her own home.
Aeon 14: The Scipio Empire is an oligarchy full of political intrigue, but Empress Diana genuinely tries to do right by her people, starting with having overthrown and killed her tyrannical father. Notably, power is intentionally divided between herself and four prelates, who have enough power between them to overthrow her if they have to. (She had planned to call for elections, but a Civil War led her to declare herself empress instead.)
Cannon Fodder: The Norgolian Empire. While definitely an empire and definitely expansionist, they're pretty fair to their own citizens.
The Culture: The Culture engages in covert social engineering missions on other planets and civilizations to help them see the benefits of joining the Culture.
Dark Shores: The Celendrial Empire. First and foremost, it's highly efficient in laws, logistics, taxes and warfare. And while it has conquered the whole continent, it does not really oppress anyone, as long as they obey the laws, pay the taxes and send their second sons to the legions. However, under the leadership of power-hungry Cassius as consul it may be heading straight into The Empire territory.
Discworld: Ankh-Morpork used to be the more traditional type of Empire, but economic dominance was more sustainable. The city-state only directly controls a small portion of land, but its economic influence throughout the continent is almost limitless, and its production is so great no one dares invade for fear of being deprived of the very tools needed for invasion. It's also the center of all information trade, giving unequaled political clout in the region.
Elantris: This is how the current iteration of the Fjordell Empire works. Centuries ago, Fjorden was a traditional empire, but it was unable to hold onto its military conquests and eventually fell apart. Fjorden's current rulers dedicated to expanding their power through cultural and religious dominance instead, and are successful enough that, despite being small when looked at on a map, their nation has gained effective control over more than half of the continent of Opelon. Having their emperor also be the head of the Derethi church helps, since it means that people who convert to Shu-Dereth are technically answerable to the Fjordell government regardless of national affiliation.
Eldraeverse: The Empire of the Star prefers to operate in various versions of this way, having noticed long ago that conquering people who don't want to be — and keeping them conquered afterwards — is expensive and problematic, whereas if you can make them want to join up, the whole conquering thing becomes somewhat superfluous, expansion-wise.
The Star Empire of Manticore is heading in this direction in the later novels, having acquired a certain taste for expansionism and imperialism, but still remaining The Good Kingdom/The Republic good guys they started as. At the same time, Solarian League, despite quite obviously cracking at the seams, is still it big time.
The Anderman Empire was always this. Gustav Anderman I's first conquest, Kuanyin, was overjoyed to have him, because they were in the midst of a worldwide crop failure and he was rich enough from his merc days to hire a cadre of scientists to cure the blight that was causing it.
The Stars, Like Dust: Tyranni is a relatively small empire of some fifty worlds, who are presented in a villainous light, although not entirely unsympathetic. The Tyranni are outnumbered "hundreds to one" by the subject populations of their empire, and must therefore resort to "devious methods" (such as assassination) to maintain their rule. Their conquest of that empire evidently involved a good bit of taking advantage of the disunity of the Nebular Kingdoms—"the opposed Kingdoms toppled one after another, singly; each waiting (half joyfully at the discomfiture of its neighbors)". But they also rule with a relatively light touch, leaving previous rulers in place to serve as vassals, and mainly concern themselves with collecting tribute—"taxes"—from the subject worlds.
The Currents Of Space: The Trantorian Empire (the polity that would become the Galactic Empire) is large enough and powerful enough to buy out a planet and arrange for the evacuation of the entire human population thereof. At this point, the Galactic Superpower doesn't need to go to war to conquer other planets; they can simply purchase them.
This series tracks as the Encyclopedia Foundation becomes larger and absorbs nearby interstellar nations while the Galactic Empire decays and collapses. Dr Asimov's Empire is explicitly modeled on The Roman Empire, so the Foundation resembles the Byzantine Empire, the Greek-centered "Eastern Roman Empire" that lasted a thousand years longer — but not exactly, as the Foundation is set up specifically to reestablish the Empire within a single millennium. By preserving knowledge of advanced technology, they gain religious dominance over their nearest neighbors. Then by using trade and economics, they further spread their influence. Leaving aside a temporary and extremely unlikely setback, it keeps evolving through multiple policies as the Foundation grows across the galaxy.
Ender's Game: While the One World Order is called the Hegemony, it is more in the vein of a necessary evil: there's a Bug War happening and someone needs to take control. At the end of the Ender's Shadow series, Peter Wiggin replaces it with the Free People of Earth, which governments opt into voluntarily and are only allowed to opt into voluntarily. It works, at least for a while (supposedly it collapsed somehow and was replaced with the Starways Congress of the later Ender books).
Malazan Book of the Fallen: The titular empire was formed mostly by way of military conquest, but its constituent states have all mostly realized that remaining in the Empire means not constantly feuding with neighbors. In Assail, a character lampshades the fact that from the perspective of the common people, the Malazan Empire is no more corrupt than the old regimes and it offers the poor opportunities they never had before. The empire is mostly a meritocracy and thus a peasant from a backwater community like him can rise up in its ranks as far as his talent and luck will allow him.
Quarters: Havalkeen is apparently one of these. There's a mention early in No Quarter that the reason the Army plans to use Bannon and Vree to assassinate a rebellious governor is to avoid the casualties, both friendly and civilian, that would be incurred via The Siege or by Storming the Castle. The Empire's Marshal states that the Empire gives "a promise of peace, order, and good government".note A phrase used in the constitution of author Tanya Huff's native Canada, and commonly used for describing its governing philosophy.
Starsight: The Superiority is one. They maintain only a very minimal military (in part because they have an extreme culture-wide aversion to violence or aggressive behavior of any kind), and instead maintain power by virtue of being the only ones who know how to make FTL drives that won't attract the delvers. They don't have to conquer worlds that refuse their commands, just cut them off from the wider galaxy.
The Tamuli: The Tamul Empire conquers other countries by usually only needing the threaten war, as it has one of the finest fighting forces in the world in the shape of the Atans, a people who through centuries of selective breeding are the biggest, strongest and most skilled soldiers ever. It then exercises authority through the existing power structures, doesn't interfere with the existing culture, religion customs or social order, imposes minimal extra taxes and the only real rule it enforces is banning war between provinces. Not for nothing are the Tamuli known in universe as "history's finest imperialists" (despite their empire being more-or-less accidental — the Tamuli didn't set out to conquer the continent, the Atans swearing themselves to them just meant that all those relatively minor squabbles that neighbouring nations have tended to end up with Atans in the the neighbour's capital and the Tamuli having another province in their empire). They don't even punish revolutionaries — if revolutionaries appear in a province they take this as a clear indication that something has gone seriously wrong in the local governance and will usually offer the job to the revolutionaries — who will discover that this is a poisoned chalice as no-one likes the provincial government!
The Traitor Baru Cormorant: The Imperial Republic of Falcrest, by its own words, never conquers anyone, because military conquest breeds diseases and discontent, and is highly wasteful besides. Despite being the known world’s foremost naval power, Falcrest prefers slower but more efficient methods of economic and cultural domination in its bid to Take Over the World: trade monopolies to seduce countries with wealth and render them economically dependent, schools to give foreign children high educations and indoctrinate them with Falcresti values, vaccinations prioritized to particular groups after first contact inevitably causes plagues... and while that's happening, Falcrest is using spies and hostages to destabilize things behind the scenes so that they can heroically step in and provide aid to the poor, suffering natives, which of course will require further occupation — with their consent, of course. What the Romans Have Done for Us is discussed, as there's no way to separate the terrible things Falcrest does to its provinces (criminalization of old customs and mutilation of offenders, eugenics programs, suppression of native cultures, etc.) from the genuinely good ones (improved education, engineering, sanitation, etc.) The Monster Baru Cormorant further shows that there’s nothing stopping them from pulling out of a territory if they decide it’s no longer profitable, and after having made themselves indispensable to the locals, leaving makes things go to hell.
The Witchlands: The Cartorran Empire has mostly expanded through marriages, alliances, and enticing vassals with treaties of protection. They've only begun to turn into conquerors very recently, as there are simply no more countries willing to ally with them left.
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