Thanks for compiling an awesome set of mods, I'm sure quite a few people will be trying it out in the lead up to Fallout 4 coming out later this year!
I just wanted to add that I had some terrible stuttering in my installation of FO3 (even just vanilla would do it, but was much more pronounced with mods added).
It wasn't the typical microstutter or "64hz" issues. It happened regardless of any settings that I used for FSE. I searched all over the place and mostly just found people resigned to the fact that the game engine is crap and therefore you just have to live with the problem.
To give a little more detail on the problem I had been experiencing, it would always happen when standing still and panning the camera around with the mouse, I could reproduce it by centering my view over certain parts of the landscape over and over.
One spot I used to test this problem is immediately after leaving Vault 101, walk over to the "scenic lookout" sign directly ahead and then center your view over the water tower that is right in front of you. As you move the view left to right slightly there would be a brief stutter every time. It may start out only being very brief (only a like 1 10th of a second), but the more you repeated the motion, the larger the stutter could become (it would end up "pausing" for up to 3/4 of a second at times).
Now, I'm still not quite sure of the cause of the problem, but I found this "mod" on Nexusmods that has fixed it completely for me. The link to the mod is:
This mod is basically just an archive of a preconfigured Fallout.ini and enboost (setup for use with GEM). I am aware that there are a lot of ini tweaks that really have no tangible effect on actual real world performance, so I'm not 100% sure which setting has helped to resolve the issue I was having, but I can say that these configs have completely removed any stuttering I was previously experiencing.
Other peoples mileage may vary, but if you're reading this and have been experiencing the same kind of stuttering problem I have described above, give these settings a try. I hope this post helps some other folks out there that have been pulling their hair out as well!