Vortex: Lacks many essential features, such as manual load order control or a virtual file system.
Nexus Mod Manager/Fallout Mod Manager: Outdated/abandoned, have no virtual file system or even dynamic movement of mods with loose files.
Mod Organizer 1: Although Mod Organizer 2 is 64bit and was designed for 64 bit games, it works perfectly with Fallout 3/New Vegas. There is no reason to use Mod Organizer 1 over Mod Organizer 2.
LOOT: As LOOT is automated, it will never fully be able to account for all the nuances of a load order, especially a large one. Incorrect load order can lead to overwriting or breaking features from mods. Load order on its own will almost never be able to fully solve conflicts, which is why conflict resolution is incredibly important.
Wrye Bash/Flash and Mator Smash: Similarly to LOOT, these programs are fully automated and will never be fully accurate. They will solve things that they may see as conflicts but it reality are intentional overwrites. They will also often miss critical conflicts.
zEdit/zClean: Neither have any real advantages over xEdit, and lack some essential features/support than xEdit has.
Merge Plugins Standalone/zMerge: Automated merging can potentially cause major breakage in mods, especially heavily-scripted ones. 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. And if for some reason you do need to merge, the safest way of merging is manually merging with xEdit.
Ordenador/DDSopt: Breaks many textures by needlessly converting/adding/resizing alpha channels, cubemaps, and mipmaps. You should not be using textures mods over 2k anyways, so nothing should even need resizing.
BethINI/New Vegas Configator: Most INI changes these programs make are placebo at best, dangerous at worst. You won't need any INI tweaks other than the ones in the guide.