Reputation
This mechanic is what separates the zeros from the heroes. Understanding reputation and factions is one of the easiest and most impactful things you can do in order to improve your game. I'll start by giving a general overview here, and then going into particularly noteworthy factions.
Overview
First, the mechanic. From -249 to 249 reputation, you are neutral with that faction. Enemies with a neutral or docile temperament will not attack you, but will become hostile if you harm them or one of their allies. This is the ideal range to hit for the vast majority of factions as most creatures in the game have a neutral temperament. For certain factions, like Flowers, this won't be quite enough and you'll need to go a step beyond as most of their members have aggressive temperament.
From -599 to -250 reputation, you are disliked by that faction. Docile creatures will still not attack you unless provoked, but neutral enemies will attack you. The vast majority of "enemy" factions start off in this range, like Robots and Seekers of the Sightless Way. Very few creatures are docile, so for nearly all factions you want to be out of this range as soon as possible.
Anything beyond -600 reputation and you are despised by that faction. Everything from that faction will attack you on sight. There is very little functional difference between being despised and disliked, so if you are not planning on becoming at least neutral with that faction at some point, just let your reputation here drop as much as you like.
From 250 to 599 reputation, you are favored by that faction. All creatures from that faction will not attack you unless provoked. In most cases, going to this point is just unnecessary as it isn't functionally different from being neutral but for factions like Flowers and Winged Mammals, this level of investment is necessary as the standout members are aggressive. Being at this level also allows you to enter holy sites of that faction without provoking them, but only Apes, Baboons, Mechanimists, Gyre Wights and Cult factions actually have holy sites to begin with.
Anything beyond 600 reputation and you are revered by that faction. Members will actively attack creatures that attack you and will not immediately turn hostile if you attack an ally of theirs. This is quite the difficult level to attain and is usually not worth the investment. For most factions, there isn't anything worth noting besides the above. However, it's worth a mention that if you're revered by the Consortium of Phyta, you can just command Asphodel to lease control of the Spindle instead of suffering any reputation penalties from that quest.
In addition to these mechanics, having a higher reputation will result in you having better prices with the merchants of that faction while lower reputation will result in you having worse prices.
Understanding this is just the start, because it's easy enough to reduce this down to "shoot for -249 reputation in nearly every scenario" and for it to actually be pretty good advice. In order to reach that upper echelon, you'll also need to understand factions.
Factions
There are far too many factions in the game for me to go over each one in detail, so instead I'll break them up into groups. After determining the groups, I'll also list each faction and the ideal reputation to hit.
Irrelevant Factions
These factions either have so few members that when you do encounter them, it will be inconsequential or the faction members are just too weak to be a threat or worth making neutral to you. Feel free to dump the reputation for these factions.
Antelopes
Birds
Cannibals
Children of Mamon
Dogs
Equines
Farmers' Guild
Highly Entropic Beings
Issachari Tribe
Newly Sentient Beings
Roots
Snapjaws
Succulents
Swine
Water Barons
Low-Threat Factions
These factions are not completely inconsequential, but are generally weaker than most creatures or simply not worth the effort to make them neutral to you. You can pretty safely dump reputation for these factions as well.
Arachnids
Baboons
Bears
Cats
Cragmensh
Frogs
Girsh
Goatfolk
Gyre Wights
Hindren of Bey Lah
Putus Templar (as a mutant)
Randomly Generated Villages
Sultan Cults
Tortoises
Trees
Trolls
Urchins
Vines
Worms
Maintain Neutrality
These factions will start off neutral to you and you generally want to just maintain that neutrality. These factions aren't particularly relevant, but since you'll be interacting with/around members of this faction, you'll want to keep them peaceful. As long as you're not breaking that -249 threshold here, you're golden.
Apes
Baetyls
Barathrumites
Cult of the Coiled Lamb
Denizens of the Yd Freehold
Dromad Merchants
Fungi
Grazing Hedonists
Hermits
Merchants' Guild
Mopango
Mysterious Strangers
Pariahs
Putus Templar (as a true kin)
Villagers of Joppa
Don't Reduce Reputation
For these factions, you don't want to take actions that will reduce your reputation with them as they teach valuable skills that you'll want to have. While you won't need to go out of your way to gain reputation with them, you should generally avoid reducing reputation with these factions in any way.
Consortium of Phyta
Daughters of Exile
Fellowship of Wardens
Villagers of Ezra
Villagers of Kyakukya
Gain Reputation
Factions in this group you are looking to increase and avoid decreasing when possible. These are lower priority than other factions that will come in the final groups, and there are some cases when you can decrease reputation when you would gain otherwise superior reputation benefits. A good rule of thumb is this: while you shouldn't go out of your way to gain reputation with these factions, if you have the opportunity you should absolutely go for it while avoiding reducing reputation when possible.
Crabs
Mollusks
Svardym
Winged Mammals
High Priority
Factions in this group you should go out of your way in order to improve. Search out legendary creatures in order to improve your faction relations at every possible opportunity. Use love injectors to water ritual these legendary creatures if they are aggressive to you.
Fish
Flowers
Insects
Naphtaali Tribe
Svardym
Unshelled Reptiles
Critical Priority
Factions here are so important you should increase reputation with them in every way possible. These factions are prime candidates for a Schrodinger page from the Annals of Qud and you should seek out any and all improvements you find. Avoid decreasing reputation at all costs, even forsaking powerful gear in order to avoid lowering reputation.
Oozes
Robots
Seekers of the Sightless Way
Mechanimists
If you paid close attention, you'll have noticed that the Mechanimists are not listed in any of the groups. This faction falls in its own special category since you can improve your reputation through offering artifacts, which is far easier than scouring the map for legendary creatures. Post Bethesda Susa, your reputation here doesn't matter very much as long as you keep it at least neutral. In fact, since legendary Mechanimists will hold Eaters' nectar injectors, there is very good reason to kill legendary members and just accept the hit to your reputation. Just be sure you'll stay neutral so that you can boost yourself out of the danger zone without being swarmed by angry priests.
Target Reputation
In an ideal world, you'll want your reputation with these factions to be at least this value. Of course, realistically you won't hit these numbers which is the point of the above categories so you know which to prioritize. This section is to answer the question of “now that I know what to go for, how far do I go?”. For most of these, the answer is to neutral but for some you'll want to go above.
Antelopes: -249
Apes: 250
Arachnids: -249
Baboons: -249
Baetyls: -249
Barathrumites: -249
Bears: -249
Birds: -249
Cannibals: 250
Cats: -249
Children of Mamon: -249
Consortium of Phyta: 600
Crabs: -249
Cragmensch: -249
Cult of the Coiled Lamb: 100
Daughters of Exile: 100
Dogs: -249
Dromad Merchants: 600
Equines: -249
Farmers' Guild: -249
Fellowship of Wardens: 0
Fish: 250
Flowers: 250
Frogs: -249
Fungi: -249
Girsh: 200
Gyre Wights: 200
Goatfolk: -249
Grazing Hedonists: -249
Hermits: -249
Highly Entropic Beings: 250
Hindren of Bey Lah: -249
Insects: -249
Issachari Tribe: -249
Mechanimists: 300
Merchants' Guild: 600
Mollusks: -249
Mopango: -249
Mysterious Strangers: -249
Naphtaali Tribe: -249
Newly Sentient Beings: -249
Oozes: -249
Pariahs: 100
Putus Templar: -249
Randomly Generated Villages: -249
Robots: -249
Roots: -249
Seekers of the Sightless Way: -249
Snapjaws: -249
Succulents: -600</span>*
Sultan Cult: 250
Svardym: -249
Swine: -249
Tortoises: 250
Trees: 250
Trolls: -249
Unshelled Reptiles: -249
Urchins: -249
Villagers of Ezra: 150
Villagers of Joppa: 50
Villagers of Kyakukya: 100
Vines: -249
Water Barons: -600</span>*
Winged Mammals: 250
Worms: -249
🗒️ Note: Succulents perform the same way regardless of your reputation with them. Water Barons have zero faction members.