The majority of mods can be found at The Skyrim Nexus
Skyrim Mods
Utilities
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LOOT
Loads your mods in a certain order to avoid crashes
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Mod Organizer
A better alternative to Nexus Mod Manager
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Skyrim Script Extender
Required for many mods
Player Homes
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Bottom of the Well
A house for a starting character. Well, less of a house and more of a slump of a well
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Kagrenac's Mountain Fortress
A (non lore-friendly) home that adds the Fortress of the Dwemer Chief Tonal Architect Kagrenac
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Scholar's Solice
A cozy home found in this list of mods called "The Junkyard"
Sounds, Voices, and Music
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Immersive Sounds - Aural Assortment
Makes magical sound effects sound better
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Immersive Sounds - Compendium
The whole Immersive Sounds collection
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Smarter Combat Music
Fixes the combat music for certain circumstances
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Sounds of Skyrim - The Wilds
Makes the wilds of skyrim more immersive
Texture and Mesh Replacers
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Ancient Falmer Armour Overhaul
Makes the Ancient Falmer armour look better
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Electrify
Makes shock magic more awesome
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Fitness Body
Makes females a bit more muscular.
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Madness Malacath
Various replacers for the Statue of Malacath
Weapon and Armour Additions
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Ancient Falmer Crown - Fix
Gives Arch-Curate Vyrthur the Ancient Falmer Crown, which was originally unobtainable, so that you can loot it off his corpse
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The Archers Arsenal - Special Arrows and More
Enriches the world of Archery in Skyrim
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Better Shaped Weapons
Makes weapons better shaped to be more realistic
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Boethiah Ring of Shadows
Adds a (non lore-friendly) artifact to the game
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Bosmer Armour Pack
Adds a unique piece of Armour specifically for Bosmer hunters
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Dagger of Vaermina
Adds a (non lore-friendly) artifact to the game
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Ghosu's Mods
Everything this modder does is awesome
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The Gray Cown of Nocturnal - Fully Functional Gray Fox Cowl
Adds the Cowl of Nocturnal from Oblivion, and does the same thing as it as well
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Heavy Armory - New Weapons
Adds brand new weapons
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Immersive Armours
Makes armour more immersive
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Immersive Weapons
Makes weapons more immersive
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Knight of Molag Bal
Adds awesome new armour for a Knight of Molag Bal
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Konahriks Accoutrements - Dragon Priest Armory
Adds various new weapons and armor involving Dragon Priests
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The Mad Maskar
Adds several new hats and masks for the player to wear with various effects
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Midnight Breed Armor - CBBE UNP 7B - Modular with 5 Colors
Adds a sexy new piece of armour
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Moon-and-Star Ring - Morrowind Lore Friendly
Adds the legendary ring of St. Indoril Nerevar that was in Morrowind
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More Interesting Loot for Skyrim
Does exactly as the title suggests
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Tribunal Robes and Masks
Adds (non lore-friendly) masks and robes of the legendar Tribunal Saints
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Anything by InsanitySorrow
Several replacers for otherwise unique weapons that had boring appearances
Quests and Factions
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Black Horse Courier Reborn
Brings back the Black Horse Courier from Oblivion that I have yet to try
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Falskaar
A huge mod that adds a new island with new quests and is fully voice acted. This is a DLC sized mod that I have yet to try
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The Lost Wonders of Mzark
A huge Dwemer based questline based on the Dwemer "Mzark" that I have yet to try
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Path of the Revenant
Adds a new quest to recover the Staff of Worms and the Bloodworm Helm
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Spectraverse - Magic of the Magna-Ge
A questline involving the Magna-Ge that I have yet to try
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The Wheels of Lull
A large quest mod that I have yet to try
Other
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A Matter of Time - A HUD Clock Widget
Adds a clock to your UI
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Air Atronachs
Adds Air Atronachs, which were only seen in Daggerfall and ESO
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Alternate Start - Live Another Life
An alternate start mod
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Apocalypse - Magic of Skyrim
Adds a crap-ton of new spells
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Armored Skeletons and the Walking Dead
Undead creatures now can wear armour
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Auri-el's Bow Enhanced
Completely re-does Auri-El's Bow's enchantments
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Azura's Shrine Temple
Adds a temple next to Azura's shrine
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Beards
Lets your character have a beard. Now you can be a lorebeard too!
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Better Docks
Why were all the docks in skyrim so empty? This fills them up
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Better Vampires
Makes vampires better by allowing you to customize several functions and adds new abilities
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Bromjunaar Extended
Bromjunaar was the capital of Skyrim during the reign of the Dragon Cult. You visit it upon grabbing Kohnariik's Mask, and this expands upon it
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Character Creation Overhaul - Races - Birthsigns - Classes - Skills - Specializations - Attributes
Gives Skyrim a class system similar to previous games
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Cloaks of Skyrim
Adds cloaks to the game.
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Community Uncapper
Uncaps your level from 100 to 10,000
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Crime Overhaul
Overhauls the crime system
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Crimson Tide - Blood
More immersion with blood!
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Dark Maneuvers - Harkon shield Undead Lords and more
Adds several new spells for vampires, and more.
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Dwemer Spectres
An amazing mod that brings back the spectre of the Dwemer like in Morrowind
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Enchanted Arsenal
Adds a shit ton more enchantments
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Extended UI
Extends the UI
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Extensible Follower Framework
Allows for more options for your followers
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Face to Face Conversation
Let's you talk to NPC's face to face like in Oblivion
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Falkreath Skyscraper
Adds a huge tower similar to Korren's Tower in Dragonball
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Feminine Running and New Dash Animation
Replaces female animation for running
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Fire and Ice Overhaul
Completely overhauls how fire and ice spells work in Skyrim
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Footprints
Gives your character footprints in the snow, as well as NPC's
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Forgotten Magic Redone
Adds spells from previous Elder Scrolls games that were cut out in skyrim
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Gold's Secrets Revealed
Changes "Gold" to "Septims" and allows you to smelt them into gold ingots
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High Hrothgar Alternate Cave Route
Gives an alternate route to High Hrothgar rather than climbing those damn stairs
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Hunting Grounds
Visit the plane of the Daedric Prince of the Hunt: Hircine's realm: The Hunting Grounds
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Immersive College of Winterhold
THIS MOD IS CURRENTLY BEING UPDATED
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Immersive First Person View
Allows you to see your own body when you look down
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Immersive NPC in the Dark
Makes using darkness more reliable for thieves and sneakers
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Immersive Player Dialogue
Exactly as the title says
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Immersive Speechcraft
Does a variety of things for your speechcraft
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Interesting NPC's
Populates Skyrim with over 250 voiced NPC's and over 50 quests. This mod is over 2GB in size.
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Jaxonz Named Save
Allows you to name your save file
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Jaxonz Real Names
Renames generic names such as "Whiterun Guard" to a real name. Lore Friendly
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JK's Skyrim
Overhauls all cities in Skyrim
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Legacy of the Dragonborn
Adds a large gallery for you to show off your collection of items, as well as adds dozens, if not hundreds of more relics for you to collect to add to the gallery
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Legendary Cities - Tes Arena - Skyrim Frontier Fortress
Adds ten historical cities to Skyrim present in TES:Arena
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Lock Overhaul
Allows you to overhaul the lock system, as well as bash locks and unlock locks via a new spell
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Lore Styles Hair Set
Includes hair styles from previous Elder Scrolls games
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Lost Enchantments
Adds enchantments from previous Elder Scrolls games that were cut from Skyrim
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MLP Moon with Phases
Adds the visage of Nightmare Moon from My Little Pony: Friendship is Magic to the moon "Masser"
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MoreHUD
Gives you more HUD options
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Morrowloot
I wont ruin the surprise ;)
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Ordinator
A perk overhaul
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Rings of Old
Adds rings from Morrowind into the games
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Royal Bloodline - Vampire Lord perk tree - abilities - and more
Does many many things in relation to vampires
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Nock to Tip
All arrows are now knocked to the tip of the bow
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Sit Anywhere
Literally anywhere
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Skyrim Enhanced Camera
Lets you see the rest of your body when looking down
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Skyrim Sewers 4
Adds sewers to various towns and cities
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Skytweak
Allows you to tweak several settings and variables in the game
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SkyUI
Required for many mods. Changes the UI.
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Smoking Torches and Candles
Candles and Torches now produce smoke
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Stones of Barenziah Quest Markers
The Stones of Queen Barenziah now has quest markers
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Take Notes - Journal of the Dragonborn
Allows for a better Journal system
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TDN Equipable Horns
Equipable horns for your character
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Telescope
Adds a Telescope
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Thieves Guild Bounty Clearer
Allows you to clear your bounty by going to the Thieves Guild like in Morrowind
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Timing is Everything - Quest Delay and Timing Control
Allows you to change the timing of certain events in the game
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UIExtensions
Extends the UI
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Unofficial Legendary Patch
The most popular patch for Skyrim that fixes many bugs and glitches
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Vanity Mirror
Change your appearance whenever and wherever you like
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Various Player Actions
Lets you do various things
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Wear Robes over Armour
Brings back the mechanic from Morrowind
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Wintermyst - Enchantments of Skyrim
Adds many new Enchantments
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World Eater Beater
Makes Alduin's fight much more fun
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Worlds Dawn - Enchanted loot and RPG attributes in Skyrim
Rewards your adventuring with a huge variety of unique and powerful loot to be found throughout Skyrim, and increases the depth of gameplay by introducing classic RPG attributes.
NSFW
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Alive Peeing
Watch your character piss
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Better males - Beautiful nudes and faces - New hairstyles
A body replacer for men
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Caliente's Beautiful Bodies Edition -CBBE-
A body replacer for females
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Edhildil's Statue Mods
This author makes statues that are sexier
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Female Werewolf
Makes werewolves more adult
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Feminine Argonian Textures for CBBE-UNP (Chameleon and Lizard
Argonian replacers for CBBE and UNP bodies
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Feminine Khajiit Textures for CBBE-UNP (Grey Cat and Leopard
Khajiit replacers for CBBE and UNP Bodies
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Mord Sith Cara Armour - 7 Base - UNP - CBBE - 7 Base BBP
Adds sexy leather armour
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Polished and Sexy Nocturnal Statue
Makes the Statue of Nocturnal sexier
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Pubic Hair Alternatives CBBE
Customize your female character's pubic hair
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Sexy mara Statue
Makes Mara's statue sexier
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Sunburn for UNP and CBBE
Gives your character Sunburn and/or a tan