New Vegas Stutter Remover: New Vegas Tick Fix is a modern recreation of Stutter Remover that works flawlessly and has many more features, such as the high FPS physics fix. There is zero reason to use Stutter Remover instead of Tick Fix, even on Windows 7.
ENBoost: New Vegas Tick Fix has much better memory management than ENBoost, and will increase performance/decrease stuttering more. ENBoost also needs a lot of system-specific configuration to work properly and can degrade performance without proper tweaking.
Zan AutoPurge Crash Protector/PCB Hotkey: Unsafe/unstable, same function is performed safely by the .INI tweaks in the guide.
Save Cleaner: Saves have not been reversed engineered like in Skyrim, this will break your save.
Performance of the Gods (or pretty much all mods with "Performance" in the title): Performance gain is placebo, disabling small clutter items with less than 5 polygons won't do anything. Also potentially dangerous if they mark the records as Deleted rather than Initially Disabled.
Mission Mojave: Heavily outdated compared to Yukichigai Unofficial Patch, will break more than it fixes and cause crashing.
Old single bug fix mods, such Reload Game Start Fix: In most cases, these fixes are included in either Yukichigai Unofficial Patch, Unofficial Patch NVSE, or lStewieAl's Tweaks, and if they are not it is most likely because of poor implementation of the fix on the mod's end and/or the thing the mod fixes not actually being considered a bug.
ENB: ENBs were never fully developed for New Vegas like they were for Skyrim/Fallout 4. They have a ton of bugs and performance issues, such as broken Anti-aliasing and objects becoming transparent. They also use a lot of vision-obscuring effects like depth of field, lens flares, bloom, and chromatic aberration to obscure the broken Anti-aliasing, which makes hem very hard to play with. They are also incompatible with New Vegas Tick Fix's memory improvements.
New Vegas Reloaded: The newest version of NVR is incredibly buggy and almost impossible to play with. If you want to use it, I recommend using the old 1.3 version instead.
4k texture mods/texture mods with 2k normal maps: The game's engine is unable to handle textures that big without massive performance loss/stuttering and/or crashing. You also most likely won't notice that big of a visual difference compared to 2k textures with 1k normals, unless you play in 1440p/4k resolution (and if you do, the performance loss will be even greater) or look very carefully at an object up close. This includes the large version of NMCs Texture Pack and Ojo Bueno. If you want to use either of those mods, use either the low or medium versions of NMCs Texture Pack (I recommend low) and Poco Bueno.
Charge's HD Texture Pack/other AI-upscaled texture packs: Generic Ai-upscaled textures that result in a very minor visual increase for a massive performance decrease. Also upscales files it shouldn't, such as normal maps and glow maps, which causes texture artifacting.
EVE: Incompatible with Weapon Mesh Improvement Mod and any other mods that edit weapon records (such as Yukichigai Unofficial Patch or JSawyer Ultimate Edition). The new explosion/critical effects can cause performance drops. EXE is an updated version of EVE that covers everything but Energy Weapons (which is the main source of incompatibility with EVE). EXE is compatible with everything.
Asurah's Reanimation Pack: Exceptionally buggy. Also makes out-of-scope changes to reload speeds and fire rates. I recommend Anniversary Animations Pack (already in the guide) and Clean Animations instead. Both are compatible with Weapon Mesh Improvement Mod.
Borderlands Inspired Numeric Damage: Outdated, replaced by Samurai Floating Damage.
Fallout Character Overhaul: Multiple broken file paths which cause missing mesh triangles and pink textures. The installer is also broken, and auto-selects patches for mods you don't have installed and installs the Glowing Ghouls file, which causes massive performance drops and save bloat. Doesn't cover every NPC in the game (plus NPCs from the DLCs or mods), so any uncovered NPCs look very out of place. It also requires the bLoadFaceGenHeadEGTFiles INI setting to be enabled, which causes performance loss due to generating NPC face textures on the fly in-game. I recommend New Vegas Redesigned 2 Revised instead (already in the guide).
Interior Lighting Overhaul: Can cause FPS drops in large interiors due to the new light sources. Also has some bugged interiors that are pitch-black. I recommend Simple Interior Lighting Overhaul instead (already in the guide).
Handheld Pip-Boys, such as the 2500: All hand-held Pip-Boys share the same issues, such as the Pip-Boy being tilted or causing your weapon to be held on the wrong side of your body. I recommend either the 2500a or 2000 Mk VI instead.
Electro City: Has broken LOD that can cause crashing. Also includes unnecessary bloat such as new NPCs and boxes full of Cateye. I recommend A Little More Lamplight instead (already in the guide).
Unnecessary Physics: Causes save bloat, since the game has to save the position of every object you move.
Vault 22 Flora Overhaul: Disables objects with the Has Tree LOD flag, which can cause crashing. Also has tons of unnecessary bloat such as new weapons, enemies, poison effects, skill books, and more. I recommend Vault 22 Flora Overhaul Remastered instead.
New Vegas Landscape Overhaul (including the Remastered version): Has deleted navmeshes and deleted objects with the Has Tree LOD flag, which will cause crashing. I recommend Enhanced Landscape instead.
Project Reality: Very poor scripting, will cause massive performance issues and save bloat. If you want a different weather mod than Altitude, I recommend Nevada Skies instead.
Project Nevada: Outdated, inefficient, bloated, and broken. Most features have modern alternatives (see the list below). Has almost 20 scripts that run every single frame, causes save bloat due to continuous quest stages being triggered, and some features either don't work or break the game (chargeable weapons, lethal headshots, and the stealth/AI changes).
Although it may seem counterproductive to install a bunch of small mods to replace one big mod, these alternatives are all more efficient and performance friendly. They are 100% safe to use, and actually work, unlike Project Nevada:.
Solid Project: Poor scripting which causes many issues, such as a multi-frame lag spike every time you start sprinting. Most features are quantity over quality, and all of the "quality" features from it have been replaced by Just Assorted Mods.
FOOK, New Vegas Enhanced Content, and Mission Mojave Ultimate Edition: Massive compilation mods like these eventually get outdated and break other mods like Yukichigai Unofficial Patch. For example, NVEC includes the old version of the Burning Campfires that causes save bloat, an old version of EVE that is even more performance-intensive than the current one, outdated bug fixes that break Yukichigai Unofficial Patch, and much more).
Unlimited Companions (or any other companion-related mods): Unlimited Companions re-compiles every script in the game and will break many mods. If you want unlimited companions, or other companion-related features like equipment managing, infinite ammo, combat-ready companions, and much more, use JIP Companions Command and Control. Before installing any mods that edit companion behavior, you should check if JIP CCC already does it.
Populated Casinos: Poorly made mod with many dirty edits/ITMs/UDRs. The engine also can't handle that many NPCs in the same area without performance loss. I recommend Casino Crowds instead.
Freeside/Strip Open: Suffers from the same engine limitations as Populated Casinos. Freeside Open has many dirty edits, and both Freeside and Strip open have deleted navmeshes.
Increased Wasteland Spawns: Causes save bloat due to using the PlaceAtMe function. I recommend Mojave Wildlife (I recommend the Vanilla No Chanced Spawns Version version) and The Living Desert (already in the guide) instead.
True Wasteland Economy: Incredibly script-heavy, will cause save bloat and deteriorate performance over time. I recommend Economy Overhaul instead (already in the guide).
DUST: Poorly made mod with almost 1000 errors in xEdit. Has a combination of deleted records, leftover null references, missing records, and more.
Sinitar's Gameplay Overhaul (or anything made by Sinitar): Sinitar knows nothing about modding, as shown by his guide that includes most of the mods on this list. SGO is full of bugs, broken features, awful balance, and Sinitar's trademark typos. Avoid anything he makes at all costs.
Any AI mods: AI mods generally just edit gamesettings, which can both break scripted sequences (such as the vault in Dead Money and Liberty Prime in TTW) and make combat more frustrating than anything. They also often lead to unintended behavior, such as the Goodsprings Settler you are supposed to save at Goodsprings Source running off into the wasteland away from the Geckos.
Any mods that edit timescale: Vanilla AI packages and scripts are based on the vanilla timescale, and can break and/or run when they aren't supposed to if the timescale is changed.
Weapon Mods Expanded/Extended: Incompatible with Weapon Mesh Improvement Mod's mesh fixes, and even if it were it would still require tons of manual conflict resolution and rebalancing.
More Perks: Broken/buggy perks and awful balance. I recommend PerkPackPlus instead.
CAGE - Continue After Games Ending: Broken and outdated. I recommend Functional Post Game Ending instead.
NV Interiors Project: Causes save bloat due to the large amount of havok-enabled items in interiors that all have their individual positions stored on the save. I recommend NV Interiors Remastered instead.
Classic Fallout Weapons: Countless broken meshes and leveled lists, will cause crashes. If you want weapons from the classic Fallout games, use WebbProductions2020's Mods (require manual conflict resolution).
Simply Uncut: Most of the stuff isn't cut content, but rather fan-made versions of concept art. Also lacks quality in many places. If you want restored content, use Uncut Wasteland instead (already in the guide).
A World of Pain: Awful balance, un-lore friendly locations, no voice acted NPCs, no room bounds/portals in interiors which can cause FPS loss. I recommend AWOP Revised instead.
Monster Mod: Awful balance, broken meshes that will cause crashes.
Honest Hearts Reborn: Re-compiles every script in the game. If you want to use it, you must clean it in FNVEdit first. Even if you do that though, there will still be a good few bugs with it.