Firstly, http://www.tesnexus.com/downloads/file.php?id=10400 works pretty well at dynamically adjusting the game's options, as opposed to 3.1 - which doesn't work at all.
I've noted that there are a few mods that are kinda odd about working reliably - http://www.tesnexus.com/downloads/file.php?id=25012, for instance, recently started working after I cleaned out my load order. In order to get the sounds working properly, though, I had to make a small patch (if anyone wants it, tell me).
Finally, if you want the magic effects present in LAME's bgShaderStandAloneEV.esp, do NOT activate the mod. There are some conflicts in it that can cause whole sections of the landscape to disappear. In addition, such conflicts are present in other mods as well. More investigation is probably needed.
Hopefully, this information is of use to somebody. It seems to me that there should be a bigger effort in regards to "porting" mods over to Nehrim - hell, I'm surprised nobody has tried to add the Nehrim UI's features into DarNified UI yet.