This is by no means an exhaustive list, and it will grow with time. The mods will be separated into two groups: Known to be incompatible and Probably incompatible. Probably incompatible means it's very likely they're incompatible, but have not been looked at. However, just because it's probable that it will be incompatible does not mean that we will help you make it compatible or fix problems while using mods on that list. You will need to speak to the mod authors to make those changes.

First and foremost Check for conflicts with FNVEdit, learn to use it, no exceptions!

We shouldn't have to say this anymore but... Unconverted Fallout 3 mods with ESM/ESP and/or animations and meshes are not compatible!

Additionally LOOT is next to useless with TTW, do not rely on it!

Finally Do not use BethINI with TTW! It WILL break your game! Regardless of what the author says!

Known to be Incompatible

1. Fallout 3 mods - TTW is a New Vegas mod, so mods loaded in FO3 will have no effect, and virtually all unconverted mods for FO3 will not work and break TTW.
2. Fallout New California - Is not, cannot, and never will be compatible with TTW no matter what anyone says and that includes patches made by smart asses.
3. Project Nevada - Anything but the core module is incompatible with 3.2+, that means Equipment, Rebalance and Cyberware are not compatible, Rebalance and Cyberware can be patched but Rebalance needs AI changing removed, Equipment can not be patched and is largely redundant with Fallout 3. There are replacements for nearly everything in PN now, check Viva New Vegas.
4. NVEC - New Vegas Enhanced Content - Uses many unused records in FNV for its own stuff, we use the same records because they're FO3 records, it WILL break TTW.
5. MMUE - Mission Mojave Ultimate Edition - Deletes records TTW needs and reuses Fallout 3 records, it WILL break TTW.
6. XFO - This mod is ancient and not even compatible with the current version of vanilla New Vegas.
7. DUST - Survival Simulator - Completely incompatible, riddled with deleted records and bad implementation.
8. FOOK New Vegas - Completely incompatible.
9. After War Nevada - Completely incompatible.
10. Fallout 4 Commonwealth mods - This includes armors, items, whatever. Leveled list problems, crashing, lag and other problems.
11. Cinemodded Fallout and Patches - Uses many old and incompatible mods, game breaking ones such as NVEC, CFW and FOOK (which are listed above)
12. Star the Wandering Courier - This mod is antithetical to our mission statement, which is to have a working, bug free as possible game.
13. Megaton Walkway - Completely breaks navmeshes in Megaton causing NPCs to teleport under Springvale, someone could fix it. (The version on the Megaton Open TTW page isn't navmeshed, but Megaton Open itself has other NPC issues and isn't entirely recommended.)
14. HeroinZero's Weapon Fixes compilation by axonis - Outdated animations and meshes. Though it's fine to use standalone reload and automatic weapon fixes. These are now fixed by kNVSE, JIP NVSE and Stewie's tweaks at the engine level.
15. YUP and other unofficial patch mods -- TTW comes with YUPTTW which patches almost all bugs and will continue to do so. TTW itself fixes bugs in Fallout 3 and New Vegas as well, sometimes supersedes fixes in YUP which are then removed from it. Regardless of what VUI+ wants, it is NOT compatible.
16. WMIM/Weapon Mesh Improvement Mod - Fix conflicts, included with TTW and more up to date (not necessary), you don't need it for WRP with TTW.
17. CZ52 mod by kouoaeha - Broken meshes and recompiles all scripts, will break TTW.
18. Unofficial Patch NVSE - Script and fix conflicts (not necessary)
19. Unofficial Patch Plus - Script and fix conflicts (not necessary)
20. Purge Cell Buffers - WILL break your game.
21. Zan Autopurge Crash Protector - WILL break your game.
22. Clear Cache Hotkey - WILL break your game.
23. Killable Children (any) - Incompatible.
24. PCB Hotkey - WILL break your game.
25. FCO - Fallout Character Overhaul - All versions are known to conflict and break TTW, do not install under any circumstances any part of it. Can be patched, but unlikely to see the light of day.
26. Fallout Who Vegas - Dialogue breaks and more, needs rebuilt to work correctly. (Your mod is a buggy mess, not TTW!)
27. Freeside Open - The original is broken, use Simple Open Freeside instead. Any other mods that modify Freeside's worldspaces may also be incompatible, check if 3.2+ TTW patches exist or for navmesh edits in xedit before using
28. Weapons of the New Millenia - There's are new versions of this that should work, YMMV.
29. More Perks - Redundant Fallout 3 perks and generally incompatible and buggy. Use More Perks Reimagined if you must.
30. Animation Replacers like WAR/Hitman's (old)/Asurahs - Completely incompatible at this time, we expect Asurah's to get a patch in the future. Incompatible with the mesh and animation fixes in TTW, irons sights, reloads for Fallout 3 weapons and other things will not work correctly. Hitman's new animations post Season 1 should work just fine.
31. CFW - Classic Fallout Weapons - Completely incompatible, breaks leveled lists in both games, broken meshes, CTDs. Use CWFR.
32. Most major overhauls to NV, like DUST - Just no, will completely break the game due to leveled list changes and/or deleted forms.
33. Anything that alters the game's timescale - Internal game functions are tied to timescale, changing them will break AI packages and other things.
34. Game Setting Tuner - Broken, bad scripting that causes save bloat and corruption.
35. MMM - Marts Mutant Mod - Could be patched but would take a lot of effort.
36. MoMod - Monster Mod - Totally broken meshes that cause CTDs and broken leveled lists. An alternative exists, but is scaled back for lore friendliness.
37. EVE - Incompatible weapon meshes and animations. The weapon retextures are available as a standalone mod.
38. PLR - Point Lookout Reborn - Has probably been fixed by now
39. Weather mods that do not have 3.2 conversions - Break water heights and image spaces.
40. ILO - Interior Lighting Overhaul - Old patch is not compatible, do not use, Sarge is working on new ones. An unofficial basic patch based on the old 2.x patch has been made by a team member, but it only resolves conflicts, it does not cover any new Fallout 3 cells.
41. WME - Weapon Mod Expansion - All meshes are incompatible with fixed animations and problems with texture sets, sound fixes and other issues.
42. WMX - Weapon Mods Expanded - All meshes are incompatible with fixed animations and problems with texture sets, sound fixes and other issues.
43. Impact - Has incompatible hard edits, but there's a scripted version that works.
44. A Familiar Friend - Pip-Boy 2500 - Use the arm mounted version or Universal Pip-Boy Customization. You must revert to arm mounted before doing Tranquility Lane and Anchorage and taking the train to Vegas the first time. Use Universal Pip-boy Customization to make this and Readius work.
45. Pip-Boy Readius - Requires Universal Pip-boy Customization to not cause issues with Tranquility Lane or the Anchorage sim.
46. Alt Start Mods - Until a 3.2+ compatible one is finished, they will break your game. Use TTW Quick Start if you simply want to skip the Vault 101 intro.
47. CAGE/CAE - Use FPGE (Functional Post Game Ending) by kazopert or FPGEL by trooper instead.
48. Any of the 2.9 optionals - Did we really need to say this?
49. Enhanced NPC Awareness - Causes random NPCs and companions after firing to become hostile to the player among other issues.
50. The Storyteller - Dirty edits and incompatible conflicts.
51. Leave Conversation - This mod force closes dialogues which breaks scripts and dialogue choices can become locked out, breaks the game.
52. Project Weaponry - Multiple incompatible meshes, all iron sights broken with TTW.
53. GRA integration mods other than jsawyerbatty.
54. Unlimited Companions - Janky mod from 2010, use JIP CCC instead
55. Weapons of the Wasteland - Causes CTDs.
56. Armor Overhauls - This includes NCR Overhaul, Legion Overhauls, Book of Steel (without patches), Spice of Life, and any other armor/outfit overhaul. Any of these will require extensive patching. Ones which use body replacers are not compatible period.
57. Increased Wasteland Spawns - Causes massive save bloat and CTD's. Creatures will multiply. Out of date and should be avoided. Use The Living Desert for a more alive wasteland.
58. Mods that edit companions looks/inventory/whatever directly - Several before 2018 or aren't made for TTW don't carry over script/package fixes and cause them to be screwy.
59. Tales of New Reno (any) - At the very least breaks certain Fallout 3 dialogues like scavenger dialogue, New Reno Ep2 breaks Super Mutant weapons and has a dupe Railway Rifle, needs more testing. Probably patchable.

Probably Incompatible

1. All TTW mods and patches made before November of 2018.
2. All weapon sound overhauls - Make edits to weapon records breaking them, can be patched.
3. Custom Race Mods - lack child races, cause CTDs. Can be patched, or switched to after certain story segments.
4. Any bug fix mods - TTW/YUP fixes bugs in both games, if you are aware of a bug which isn't fixed let us know and we'll fix it if it's possible in a clean way. Fixes in NVSE plugins are fine.

Mods with minor incompatibilities

1. New Vegas Bounties II - some of Dogmeat's dialogue is hijacked for Guts, Hermit is fixing up all of someguy's mods
2. Russell - Ghoul doctor from Caruthers Canyon will walk to and appear in Underworld due to reused marker/package, apparently breaks Fallout 3 Scavenger dialogue
3. VUI+ - Gives user message to install YUP - Don't install YUP, TTW comes with TTWYUP Probably resolved by now.
4. Ultimate Ulysses Companion and Race - Edits Caesar's Fort script to set up new dialogue with Ulysses after Caesar is dead and overwrites TTW's own changes to it, nothing super bad and trivial to patch.

Someguy's mods are all in the process of being remastered and will have compatibility patches for TTW.