You may be wondering why some mods/tools aren't in the guide, or are looking to add your own mods. If so, please reference this list:
Vortex: Lacks many essential features (such as manual load order control) and has some critical bugs.
Uses Symlinks instead of a UVFS like MO2 (see here for a comparison). Probably the second best mod manager, but there is literally no reason to use it over MO2
NMM: Lacks many of the same features as Vortex, but gives the user slightly more control. Also prone to the same bugs such as failing to install a mod completely.
FOMM: Pretty much the same story as NMM
MO1: MO2, even though designed for 64bit games, works perfect for New Vegas
LOOT and automated conflict resolution (kind of): Automated tools will never be able to manage a large load order well on their own. For small (sub-50 mod) load orders, they will suffice.
However, if you use any large amount of mods, the only way to ensure perfection is looking at conflicts in xEdit, sorting your load order to minimize conflicts, and then creating your own conflict resolution to cover what can't be fixed by load order adjustment.
GECK Powerup: No longer supported and is obsolete with GECK Extender
zEdit/zClean/zMerge Has no real advantages over xEdit and lacks the essential features/support that xEdit has. zMerge is still the best automated merging method, but automated merging can potentially cause many unforeseen problems. If you are so close to the 255 plugin cap that you need to merge to get below it, you should look to remove mods instead. Odds are that many mods are not fully compatible with one another. Even if you don't want to remove any mods, manual merging with FNVEdit is still ta much safer way to merge than zMerge.
Ordenador/DDSopt: Breaks many textures by needlessly converting/adding alpha channels, cubemaps, and mipmaps
BethINI/Configator: Most INI changes are placebo at best, dangerous at worst. You really won't need any other INI tweaks than the ones in the guide
NVSR: NVTF is a modern recreation of NVSR that works perfectly and has many more features, there is no reason to use NVSR over NVTF. The following settings are broken in NVSR:
ENBoost: NVTF has better memory management and will increase performance/decrease stuttering better than ENBoost and is incompatible with some of NVTF's optimizations. ENBoost also needs a lot of system-specific configuration to work properly and can degrade performance without proper tweaking.
Zan AutoPurge Crash Protector: Unsafe/unstable, same function is performed safely by the .INI tweaks in the guide
PCB Hotkey: Unsafe
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 random clutter items with less than 5 polygons isn't going to do anything. Potentially dangerous if they use Mark for Delete instead of Initially Disabled
Mission Mojave: Breaks more than it fixes, will cause crashes, very outdated, far inferior to YUP
Pretty much any old single bug fix mod, such as Reload Speed Game Start Fix: - In most cases, these fixes are included in YUP/UPNVSE/lStewieAl's Tweaks, and if they are not its most likely because of poor implementation on the mod's end or the bug the mod fixes not actually being considered a bug
MTUI: Old and obsolete, and has a lot of problems
Unified HUD Project - uHUD: Abandoned by the author in favor of UIO
No Dialogue Tags (NVSE) (DLC - TTW - Mods): Hides all text in brackets, including Christine's dialogue in Dead Money. Use the updated, ESPless implementation in lStewieAl's Tweaks instead