If you plan to stay naturally aspirated (no turbo or supercharger) then there is very little difference between the three you listed. Stillen seems to be the most popular, followed by the JWT pop-charger. I have only seen a couple weapon-r intakes installed. I wouldn't bank on any customer service from Weapon R while the other two actually have a service department and installation shops.
In terms of power gains, all three of them would benefit from having your ECU tuned, but I would do that only after you are finished with all intake & exhaust mods you might plan to do. Best thing for you to do is try to listen to each one installed to see what you like before deciding. Most of the change you get will come with the sound of the motor... maybe just a bit more response.
According to my research, on the VQ35DE natural aspirated with no mods, the Stillen produces the most HP and Torque gains over OEM.
Yeah I had a weapon R in my 1993 Z24 and it sucked. It always kept coming lose no matter how hard I would tighten it and the air filter was garbage. I have a stillen z tube on my FX with a K&N drop in and runs just fine and looks good. Havent had any problems or complaints with it.