I'd skip FOMM as it's rather old and relies on its own format, FOMOD, which isn't used anymore really. NMM works fine and is easiest to use, but you'll have to repack certain mods to get correct installs (i.e. mods that come with optional folder structures and such). MO is the most complex and advanced installer - I haven't used it, but if you take the time to learn it, it's apparently very good. A third option is BAIN with Wrye Flash, but it also often needs repacking to set up mods correctly.
In short, I'd go for NMM but pay attention to how the archives are set up. If it's just an ordinary set up: "textures", "meshes", "esp", it works fine. If it has "optional textures", "for FNV", "for F3" and folders like that, you'll have to follow the readme and repack it so it can be installed correctly with NMM.
Don't use LOOT for F3, use BOSS.
Edited by Arkngt, 11 June 2015 - 10:51 AM.