[x] 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.
[x] NVEC New Vegas Enhanced Content, uses many unused records in FNV for it's own stuff, we use the same records because they're FO3 records.
[x] Yukichigai Unofficial Patch 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.
[x] Weapons of the New Millenia, patch in progress, iron sights are off due to animation fixes and leveled lists need rebuilt
[x] More Perks, redundant Fallout 3 perks and generally incompatible and buggy.
[x] Animation Replacers like Weapon Animation Replacer WAR, Hitman's 1st Person Weapon Animation Overhaul, Asurah Reanimation Pack, 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.
[x] Point Lookout Reborn, it has broken scripts and dirty worldspace/cell edits. It can be patched/reconverted for TTW 3.2+.
[x] Interior Lighting Overhaul, the old TTW patch is not compatible with 3.2+, do not use. A new patch is being made.
[x] Weapon Mods Expanded, all meshes are incompatible with TTW's fixed animations. There are also problems with texture sets, sound fixes and other issues.
[x] Weapon Mod Expansion, all meshes are incompatible with TTW's fixed animations. There are also problems with texture sets, sound fixes and other issues.
[x] Impact, weapon edits are incompatible, it can be patched. There is a scripted version that works and can be used instead.
Source: Mods Incompatible with 3.2+