It's not particularly popular, only a few modding communities have really embraced it for a few reasons, but I think it could be useful here. This is primarily because this is a very "stupid" program. It's basically an automated, archiving copy paste front-end. You just drop the exe in your root folder, make a "MODS" directory in the same place, put your desired mods into that directory, and run the program. The mods must be in their own directory within the mods directory (name those directories whatever you wish - preferably the name of the mod), and make sure that the files within are not zipped and are set up explicitly where they must go. If you want to install a script mod for AP named "MyExampleMod", then the setup should look like:
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(YOUR GAME DIRECTORY)\MODS\MyExampleMod\
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Furthermore, and the reason why this is useful, is that when enabling a mod it will make a record of all the files being copied and where they went, and will back up any files that are overwritten. If you want to remove the mod you just tell JSMGE to do so and it will delete the files and restore the originals if applicable. This is similar to what the plugin manager does, but as I mentioned it is much "stupider". It does only this and nothing more. You do not have to worry about what kinds of nasty things it might be doing to your Litcube's Universe install. It's simply a more convenient way to keep track of what scripts you may have installed and make it easier to remove them if desired. I've seen a few script packages with bundled .bat files that aid in deleting their core files, so I know that at least someone somewhere may have a use for this, since this program basically does that, but does it better.
The other thing this program does is allow you to save preset loadouts of mods. If desired you could load a whole bunch of scripts into LUV with this thing, save that preset, and switch between that heavily modified LUV loadout and the default LUV loadout in one click. Or you could do it in 10 clicks by enabling each mod individually, since this feature is just a batch job for convenience.
Lastly, when you try to enable a mod that overwrites the files of a previously enabled mod, JSMGE will warn you of this. If you tell it to do so anyway it will overwrite the other mod's files (after backing them up of course). If you tell it not to overwrite them, the whole mod will not be enabled. This should not ever really happen in X3 since most of the time scripts from different mods have different names, but in some other games this is a very real problem. It's also a good way to keep track of patches.
I would not recommend using this for use with .cat and .dat files unless you know what you're doing. Remember that it is not smart enough to do any kind of "fake patching". It just copies things.
Here is the download: http://www.gamefront.com/files/21681483/JSGME.7z
It's a 7zip package, so if for some reason you don't have 7zip installed you can get it here: http://www.7-zip.org/download.html