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I have a friend that uses NMM and says he's had no issues so Iunno.
FOMM has the advantage of being the oldest, so it is the most stable and "mature" of the three. It is reasonably simple to use (it has a bit of a learning curve, but nothing major) and almost all of the mods on the Nexus will work with it (might be all of them, but I really didn't feel like installing 18K mods to test that). Its major disadvantage is that it is pretty much tied to the Fallout games, so you need multiple mod managers if you play other moddable games.
NMM is the middle child. Its major advantage over FOMM is that it is flat out simple to use, works with most of the Elder Scrolls and Fallout games (and several others), and was developed by the people who are hosting the mods anyway, so it talks to their servers quite well. Its major drawbacks are its simplicity and its need to work with multiple games. As most players who have tried it have discovered, it does a decent enough job of managing mods. But it does come up a bit short if more granular control over mod content is needed. Most will not run into this problem to any appreciable degree, but it can be a problem for some.
Mod Organizer is the new one. In my mind it has a major advantage over both FOMM and NMM in its ability to provide a degree of granularity that the others lack and the fact that it doesn't actually install anything to your Data directory, so your installed game stays about as close to vanilla as is possible. This makes it extremely easy to swap mods in an out (messing up saves is still possible, though), but it has a fairly hefty learning curve, which can be a major turn-off for some. If you have mutiple games installed (FO3, FONV, Skyrim, and FO4, for example), each requires its own installation of MO. To be clear, it might be possible but I have not found a way to make a single installation work for all four games simultaneously.
I have not tried using Wrye Bash (well, Wrye Flash if we're speaking specifically about FONV) as its learning curve seems pretty daunting, so will leave it to someone else to address its advantages and disadvantages. I can say that it removes the 255 cap for the number of mods you can have installed and has its own methods of resolving mod conflicts, but I can't say much beyond that.
What I can say is that I currently use NMM as my manager of choice until I get to the point where I need more granularity in my mod management than it can provide. At that point, I prefer to go with Mod Organizer in preference to FOMM.
You're welcome. They are all good at the basics, so if that's all you need, NMM is a good choice because of its simplicity. It's when you need to go beyond the basics that the differences start to appear.
It doesn't remove the cap as much as it lets you combine separate mods into a single bashed mod, thus freeing up some of those 255 slots for other mods. I'm sure there is a practical limit to it somewhere, but since I only run with about 100 mods at a time, it has never been a problem that I've needed to deal with.