I thought of this due to the fact that I got tired of going to servers and having them use custom studs that break shaders (I'm looking at you squidey's studs).
This is really ruining the shader experience, and I never really thought about it until I got a new gpu that could run shaders at max at 60fps.
One of the reasons old studs like those break shaders are due to them not having proper transparency.The best way to show an example of this is to show you the brickTOP.png
Below is an example of the old 125% studs, notice how they are not completely transparent.
And Here is how I fixed the 125% studs, by increasing transparency and leaving darker corners.
In a nutshell, to fix the studs, you just need to remake the stud at a even greater transparency, and just leaving a certain corner darker.
UPDATE : I just found out textures that cover brickSIDE and brickBOTTOM are affected as well.
If your textures use custom bottom and sides, I would suggest fix them or refrain from using.
UPDATE 2 : Here is a list of the broken and studs that are compatible with shaders :
Broken Stud List :
Tron studs - Might be fixable
Squideey's old - obsolete, use ZAPK's
Squideey's old Lego - Obsolete, replacement needed
Squideey's old 2- Obsolete
Squideey's New studs - obsolete
NoGlow - Maybe fixable?(Might break effect though)
Manty's studs - obsolete
Lego stud - Obsolete, replacement needed
Furling's - Completely broken
Cell shaded - Fixable
Brickland - Kind of still works
Blankland - Fixable
Working Stud List :
Zapk's Studs
Vita's Studs
Tristian Luigi's Studs
Ethan's Studs
Line Studs
125% Studs
Here is a link to the Brick Texture Replacer and the many studs you can find.
http://forum.blockland.us/index.php?topic=239713.0