http://cs.elderscrolls.com/constwiki/index.php/TES4Edit_Cleaning_Guide.
These are posted with the original author's (Brumbek) explicit permission. They can also be found on the CS Wiki guide linked above.
Mods That Need Cleaning
1em_Vilja (v3.0.1) [11 ITM, 0 UDR]24HrArenaAliveV2.esp300_Artifacts.esp300_Lore_Dialogue_Updated.esp300 Regal Imperial City 2.esp [0 ITM, 130 UDR]300_White Stallion 4.esp/Feudal Empire [version 4.4, see crucial note below this list!]A Blades House.espAddendum - Diabloblivion.espAdenseEpicDungeon.espAdonnays Elven Weaponry.espAlchemistsCave-COBL.espAliveWaters.espAliveWaters - Koi Addon.espAliyah.espallinonebasemant_COBLnoCM.esp [2 ITM, 0 UDR]All Natural - Real Lights.esp [Version 1.1] found zero ITM, 3 UDRAmajor7 Imperial Furniture.espAmbientTownSounds.espApachii_Goddess_Store.espApachii_Heroes_Store.espArcana Restored.esp [zero ITM, 3 UDR]Artefacts of the Ancestors.esp [has wild edits, German names, needs manual cleaning too]Artifacts.esp [1 ref to undelete]Atmospheric Oblivion.espAuriel's Books.espAyleidArrows.esp bartholm.esp 211 ITM, 553 UDRBD&R - Deepgrave.espBeautiful_Women_NiceOnly.espBeldaElysium.esp Benirus Manor Remade.esp Better Clocks.espBHC_Expanded.esp Blood&Mud.esp 36 ITM, 401 UDMBob's Armory Oblivion.esp [Version 1.1] found 6 ITM, zero UDRBook Jackets Oblivion.esp C&C - The Blackwood Company.esp Castle_Seaview.esp CDEP-UnderpallCave.esp cf_Improved_Barter_Gold.espChoices and Consequences - MMM.esp --> Latest version is cleanChoices & Consequences - OOO.esp 0 ITM, 10 UDRChoices and Consequences.espCliff_BetterLetters.espCliff_CountyNames.esp ClocksOfCyrodiil.espCobl Glue.esp [Version 1.73] found zero ITM, 14 UDRCompleteMagePack.espCrowded Roads Advanced less crowded.espCrowded Roads Revisited.esp [Version 1.1] found 4 ITM, zero UDRCybiades.esp 2 ITM, 0 UDRCyrodiil Border Regions 1.2.esp [not recommended to use this, use .ini tweak or Bash]Cyrodiil transportation network 1.3 WZ.esp(DC) Sutch Reborn.esp 8 ITM, 0 UDR DarkLeatherArmor.espDarknessHollows.esp DeadlyReflex 5 - Combat Moves.espDLCBattlehornCastle.espDLCFrostcrag.esp 73 ITM, 94 UDRDLCHorseArmor.esp 3 ITM, 0 UDRDLCMehrunesRazor.esp 21 ITM, 15 UDRDLCOrrery.esp 11 ITM, 2 UDRDLCSpellTomes.esp 40 ITM, 0 UDRDLCTheivesDen.esp 5 ITM, 135 UDRDLCVileLair.esp 26 ITM, 1 UDRDremoraCompanion.espDuke Patricks - Fresh Kills Now Alert The NPCs.espDwarven Mines.esp 45 ITM, 0 UDREcho_ChapelChant.espEiAmod.esp emperorface.espEnhanced Daedric Invasion.espEnhanced Quest Roleplaying.espeyja.espFightersGuildContracts.esp First Person Messages.espFrancesco's Optional Chance of Stronger Enemies.esp [SI version] found 3 ITM, zero UDRGift of Kynareth.esp [3 refs to undelete]GlenvarCastle.espGrandmaster of Alchemy.espGTAesgaard.esphackdirtabyss.espHarvest [Flora] - DLCFrostcrag.espHarvest [Flora] - Shivering Isles.espHaunted_House_v1.5.espHauntedLairMod.esp [Recompile All mod]Heroes of Cyrodiil.espHoarfrost Castle.esp [Version 1.2.2] found 4 ITM, 730 UDRHouseMapMarkersOnlyBought.espIllusionary Summons.espImmersive Travelers.esp [Version 1.0] found 8 ITM, zero UDRImpeREAL City Unique Districts – xxx [all versions should be cleaned]ImpeREAL Unique CastlesIOM - Arena.espIvellon.esp [Version 1.8] found 9 ITM, 13 UDRKragenir's Death Quest.esp 3 ITM, 0 UDRKnight of Skeleton.espKnightlyArmory.espKnights.esp found 121 ITM, 257 UDRKvatch Aftermath (all versions new and old)Kvatch Rebuilt.esp [Version 1.1] found 26 ITM, 4 UDRLegendary Abilities-Shield MOJ.espLegendary Abilities-Reflect MOJ.esp [5 deleted, 0 undeleted]LetThePeopleDrink.esp [Version 2.5] found 9 ITM, 152 UDR [Cleaning fixes potential CTDs]LetThePeopleDrink-Cobl.esp [v2.5, 9 removed, 152 undeleted]LetThePeopleDrink-fountainonly.esp [v2.5, 6 ITM, 93 UDR]LetThePeopleDrink-fountainonly-Cobl.esp [v2.5, 6 ITM, 93 UDR]Living Economy - Items.espLost Paladins of the Divines.esp [Version 2.0] found 6 ITM, 3 UDRLostSpires_TheOrderofNibenay_patch.espLostSwordOfTheAylied.espLyn-StoriesFromTheSeaMod.espLynges_Thieves_Highway-10256.espMalevolent.espMannimarcoComplete.espMannimarcoRevisited.esp [gives error upon undelete about REFR:0000CC06, still saves ok]MD Saddlebags v3.0.espMidasSpells.espMighty Umbra.esp [1 dirty edit]MIS.espMODAssassinsCreed2_Revisited.espMoriarcis.espMorrigan Swords Axes and Shield by Jojjo v1_1.espMounted_Spellcasting.espMystery of the Dulan Cult.esp (Standalone plugin)Naked Nord.esp 18 ITM, 0 UDR [Includes single wild edit, so manual cleaning required]Nanaelas Heartbreak.espNascosto Isles 3.espNew Frostmourne Sword by Jojjo v1_0.espNew Potions by Tealpanda.espNew_Sheoth_Palace_LOD_fix-10076.espnGCD pluginsNNWAREAyleidDungeons_Series1EV.esp NNWARE06-RhyeliaEmeroEV.espNo psychic guards v1.2.espnoDem's City Life.espOBSE-Storms & Sound SI.esp [45 removed, 0 undeleted]Origin of the Mages Guild.espP1DSeeYouSleep.esp [Version 1.5.1] found 7 ITM, zero UDRpale_rider's Paladin Equipment_unenchanted_eng.espPersonalPackGuars.espPhoenixEquipment.espPJs Spell Compendium - Spell Requirements.espPortable Campsite.espProgress pluginsRainbows.esprealistic water.esp [ITM: 5, UDR: 0]Reaper's waterfront.esp [ITM: 14, UDR: 60][NOTE: Standalone version only, BC integrated version is clean]rebornaylieds.espReznod_Mannequin.espROHJ2.espRoleplaying Dialogues.espRomancingAhnassi.espRTT.esp 32 ITM, 3 UDRRuin.espRuins of Tarnesia.esp [Version 1.0] found 4440 ITM, 1 UDR + ideally needs manual cleaning tooSalmo the Baker, Cobl.esp [34 removed, 0 undeleted]Sauron_Armor_Chest.espSB IC Palace Tower Light Mod v1.1 - Constant Yellow Light.esp found 2 ITM, zero UDRSecure Guild Chest.espSentientWeapon.espShadowcrest_Vineyard_COBL.espShdw_Armor Set_Sotonhorian.espShiveringIsleTravellers.espsir_balin_mod.espSK_Berserk_v0.6.espSlof's Horses Base.espSolace.espSonia.espSoT_TheOrderofNibenay.esp [Has a lot of wild path grid edits too]Spells and Enchanting at guilds.espStar's Fury.espStokerWolff.espStorms & Sound.espsunk ships.esp [135 removed, 34 undeleted]Tales from Elsweyr Anequina.esp 0 ITM, 224 UDRtda_Armoury.esptda_WitchKingHelm.espT.I.E4MODS.espT.I.E4MODSOOO+FCOM.espTamrielTravellers4OOO.espTemplar Fortress.esp (50 ITM, 892 UDR)The Ayleid Steps.esp [Version 3.4] found zero ITM, only 1 UDRThe Lost Spires.espTheElderCouncil_TempleOfTheOne.espTheForgottenShields.espThe Imperial Water - BETTER CITIES.espThe Mystery of the Dulan cult.espTheOubliette.esp theivery.espTheStorytellersBrotherQuest.espThieves Arsenal.espTOTF.espTR_Stirk.espTRoN.espTyrael Companion.espUFF & RM Gold and Silver Daedric Armor.espUnderdarkSaga.espUngarion1TheWelkyndSword.espVAs Better Gold with no Menu Icon.esp [no version number] found zero ITM, 1 UDRValley_View_Estate.espVampire Hunting - Order of the Virtuous Blood.espVaultsofCyrodiil.espVerwen Brewery UL_AY_AC Compatable.esp [1 ref to undelete]VHBloodlines 1.2.esp [v12, quite a lot to clean]Visually Enhanced Arena.espWeaponsOfTheNine.espWeye.espWest Roads [Version 1.3] found 5 ITM, 10 UDRWindfall.espwitchkingsword.espWOTFH_1.3.esp [error when undeleting records is OK]Your_Personal_Museum_Updated-9300.esp
Special Cleaning Instructions:
300_White Stallion 4.esp
Requires custom TES4Edit work to fix errors or it can’t be saved. It's too complicated to list here, but it has to do with editing REFR:00092EC9 so that it uses the Upper version of the door and moving the door into the correct position. Copy the coordinates from REFR:020014BE then delete REFR:020014BE. This also applies to the renamed Feudal Empire version.
While we're talking about White Stallion/Feudal Empire, this mod also has a LOT of errors in the AI Packages. They currently have no faction assignments and need to be updated. You can open the mod in the Construction Set and go to AI Packages and find all the ones with null parameters. Change those to have the following two conditions:
Target no, GetFactionRank, LeyawiinFaction, >=, 0.00 AND Target no, GetFactionRank, KnightsWhiteStallion, >=, 0.00
If that is too much for you, you may be better off not using this mod.
Mods That Are Already Clean
1AzuSeraphimSet.espAlchemy Book.espAlir'sArmor.espAll Natural.espAll Natural SI.espAll Natural - Real Lights.espAlluring Potion Bottles v3.espAlyeid Loot Extension.espAndragorn_Weapons_Armors.espAnduril Reforged.esp [Version 1.31]ArmamentariumArtifacts.espArmamentium female.espArmory of the Silver Dragon.espArren.espArtifacts - ArmaCompleteAddon.espArtifactsFemaleArmor.espAsharasCMPartners.espAT2 01-Shiki Armor Set.espAT2 02-Shiki Armor Set.espAtmospheric Oblivion.espattack and hide xxx v2.1.espAudaciousMagery.espBedrolls-OBSE.espBetter Cities (all files)BetterCoins.espBlackLuster.espBookCollisionTest.espC&C - The Blackwood Company - OOO.espCapesandCloaks.espCastle Redwort.espChapel Shop.espChaseCameraMod.espCobl Races TNR.esp [Version 1.53]Cobl Races TNR SI.esp [Version 1.53]Cobl Si.esp [Version 1.63]CM Partners.espCybiadesDungeon.espDACompilation_GO_SI_APN.espDA Sprint.espDAValeriaCuteElf.espDeadly Reflex Bow Sway.espDetect Life Shader [New].espDragonKnightArmor0.9.espDread Knight Armor.espDropLitTorchOBSE.espDS Flaming Arrows.espDungeon Actors Have Torches 1.6 CT.espEgress.espElsweyrAnequina.esp [Reports of ITM and UDR are all false positives. The mod is clean.]Enhanced Economy.esp [Version 5.1] Author: TheNiceOneEnhanced Grabbing.espEnhanced Hotkeys.esp [Version 2.1.1] Author: TheNiceOneEnhanced Seasons.espEnhanced Vegetation xxx.espEnhanced Water v2.0 HDMI.espES4_Alchemists Reference.espEthereal - Eyes.espEVE_KhajiitFix.espEVE_KnightsoftheNine.espEVE_ShiveringIslesEasterEggs.espEY_BM_Armory.espExterior Actors Have Torches 1.3 CT.espFastEquipping.esp [Version 1.01]FineWeapons for OOO.espFormID Finder4.espFort Akatosh Redux.espFrancesco's Optional Chance of More Enemies.esp [SI version]Francesco's Optional Chance of Stronger Bosses.esp [SI version]Francesco's Optional Leveled Guards.esp [SI version]Get Wet.espGet Wet - just droplets.espGGValeria2_0.espGhost Rider Helmet.espGrimbotsSpellTomes.espGuards of Cyrodiil Redux.espHarvest [Flora] - DLCVileLair.espHeartOftheDead.esp [Version 6.5]Hemingweys Capes.espHigher Thieves' Guild Fence Amounts.espHUD Status Bars.esp Author: TheNiceOneicPlayerHome.esp [no version number] Author: StrotiImmersiveWait.espImpeREAL Empire - Unique Forts.espImperial Furniture Renovated.espKDCircletsOOOOptimized - Loot Only.espkuerteeCleanUp.espKvatchRankFix.espKyoma's Journal Mod.espLich King's Helm v1_0.espLoadingScreens.espLoadingScreensAddOn.espLoadingScreensSI.espLoths Blunt.esp (as of 3.0.1+)Loth's Blunt Weapons for Npcs.esp [Version 3.0.1]Mage Equipment.espMaleBodyReplacerV4.espMap Marker Overhaul.esp Author: TheNiceOneMap Marker Overhaul - SI additions.esp Author: TheNiceOneMergedMaps.espMiniMap.espMIS New Sounds Optional Part.espMMM-Cobl.esp [Version 1.73]Moonshadow Elves - Sc.espMorrigan Armor Set v1_0.espMorrowind Robes and Dresses for HGEC.espMystery of the Dulan Cult.esp (Better Cities replacer plugin)Natural_Habitat_by_Max_Tael.espNicos Scimitars Back.espNight Knight Armor.espNightshade_Armor.espNo More Annoying Messages.espOL_MyBrumaFireplace.espOld Crow Inn (as of version 1.5)OOO 1.32-Cobl.esp [Version 1.32]Open Better CitiesOTEP - Aleswell.espP1DkeyChain.espPlate of the Shadow.espPowerAttack Voicemod.espPowerAttack Voicemod - The Shivering Isles.espPTRoamingNPCs.espQuest Award Leveller and DLC patchesQuest Log Manager.espRealisticForcexxx.espRealisticMagicxxx.espReal Lava 1.3.espRealSleep.espReneersNotesMod.espReznod Mannequin.espRingwraithArmorSteel.espRustyItems for OOO.espSaerileth.espScript Effect Silencer.espSlof's Oblivion Robe Trader.espShadowWatcher_HGEC_v2.espShivering OOO.espSM_COBL.esp [Version from Supreme Magicka 0.90b6 download]SM_DeadlyReflex.esp [Version from Supreme Magicka 0.90b6 download]SM_DLCSpellTome.espSM_EnchantStaff.espSM_MMM.espSM_OOO.espSM_Scrolls.espSM_SigilStone.espSM_ShiveringIsles.esp [Version from Supreme Magicka 0.90b6 download]Smite of Order.espSPB Mercenary Armors.espSpell Delete.espStarX Vanilla Vampires Revised.esp [Later versions have removed the NULL refs.]StealthOverhaul.espStopDarkBrotherhood.espSupremeMagicka.esp [Version 0.90b6]Syc_AtHomeAlchemy.espSymphony of Violence.esptalkwithyourhands2.espTamriel Resource Pack.espTamrielTravellerAdvscript.espTamrielTravellers Cosmetics Cobl or RBP.espTamrielTravellersItemsCobl.espTamrielTravellersItemsnpc.espThe Power Attack Voice ModToaster Says Share Faction Recruitment.espToggleable Quantity Prompt.esptrfjBladeMasterSword.esptrfjSolarisStaff.esptrfjSpiderGreatsword.espTRN One of the GangTyrael Armor.espUFF & RM Black Plate Armor.espUnderworld Armor.espUnique Landscapes mods (all of them)Unofficial Oblivion Patch.esp [Version 3.3.3]Unofficial Shivering Isles Patch.esp [Version 1.4.0]Update My Statue.espVanityCameraSmoother.espVASE - Cyrodiil for MMM.espVASE - Vanilla SI.espViconia.espVillages1.1.esp [Version 1.1b is clean. Not recommended to use previous versions, which are still dirty.]Visual Health Indication, Cobl.espVOILA.espWarglaives by Jojjo v1.0.espWeapon Expansion Pack for Oblivion Enthusiasts.esp Willful Resistance.espWindowLightingSystem.esp [Version 5.3.5]XiaNewAmuletsV1.espza_less_NPC_conversations.espArthmoor's mods...such as...Cyrodiil Travel ServicesFaregyl VillageNew Roads and Bridges RevisedOpen CitiesOpen Cities New SheothRAEVWD Cities.espRAEVWD Imperial City.espRAEVWD New Sheoth.esp
Mods That Should Not Be Cleaned
ArmamentariumArtifacts.espBG2408's mods (LAME, RBP, Integration)EXCEPTION: bgIntegration.esp contains a single deleted reference, but do nothing beyond addressing that.FCOM (None of the .esp/.esm files should be cleaned)Mart's Monster Mod - City Defences.esp (author says to not clean)Mart's Monster Mod - Gems & Gem Dust.esp (author says to not clean)Mart's Monster Mod - Hunting & Crafting.esp (author says to not clean)Oblivion WarCry EV.esp [Version 1.09] (do not clean core FCOM mods)Oscuro's_Oblivion_Overhaul.esm (do not clean core FCOM mods)Oscuro's_Oblivion_Overhaul.esp (do not clean core FCOM mods)Personality Idles - Modified version.esp (author confirmed that cleaning breaks functionality)SM Plugin Refurbish (Battlehorn and ThievesDen, specifically, but this goes for all the plugins) [contains dirty dialogue edits that are intentional for mod functionality, do not clean]SupremeMagicka.esp [Version 0.90b6] (Do not clean beyond what the author cleaned already)
Oh, and please don't ask for implicit dependencies to be added for every mod here, I would have died three times over before I finished with that.
Thanks to:
Brumbek (For writing the guide)
Tommy_H (For reorganizing the lists)
ElminsterEU (For TES4Edit, none of this would be possible without it)