This is a list of bookmarks that I compiled while I went down this path. This list is to help anybody just starting to try to understand how to fix games. This cuts through the miles and miles of text and discussion to hit most of the important pieces for learning. These are sorted in a rough order of importance, but there is some overlap.
I think I've read nearly everything posted publicly about fixes, but if I've missed something, please let me know in the comments and I'll update the list. If you just can't work something out, you should ask for help in the main Helix thread.
NVidia whitepapers on how 3D works and underlying principles
NVidia whitepaper on how 3D works, and how they create 3D. Really need to understand this to make any fixes. Slide 49 gives the fundamental formula for how things become 3D.
NVidia whitepaper on 3D Vision Automatic, with background on how the driver automatically creates 3D, and some things that can go wrong.
NVidia whitepaper talking about the stereo unprojection problem, and how to fix it. This is typically what goes wrong with shadows.
Starting point for learning to use Helix debugger and create basic fixes
Where it all began, first link with details on how to use HelixMod. Includes details on how to use the debugger to find shaders, and how to change the keys used.
eqzitara's guide for how to remove broken effects. Removing effects is easier than fixing them, and is often all that is necessary.
Helix tutorial on how to apply a fix using the stereo texture to get separation and convergence.
Helix's extensive update to the dlls, to add the ability to separate textures out, and thus be able to fix shaders without impacting other pieces like the HUD. Also details how to save Presets that can then be used in shaders with if statements.
Mana84 tying together the details into how we are applying the NVidia formula using the code that Helix provided. Explains how the separation and convergence come from the stereo sampler as a 'trick' by the driver.
Examples of how to do some basic fixes
eqzitara tutorial on how to convert from shader model 1.1 -> 3.0, and apply the texture fix.
Chiz1 question about getting an error in the log, and Helix's answer for how to fix it.
eqzitara comment for how to properly kill a shader. Can't be empty or it will crash.
3d4dd working through a fix for Miasmata with eqzitara and DHR to fix sky and push HUD into screen. Also set up for Helix presets to allow for aiming to change depth.
eqzitara comment on how to use Helix Lua script to autofix a lot of UDK games:
mana84 description of how to make something more transparent. This is a good example of how UI can be tweaked without exactly being a fix.
Helix comment on using the profile setting feature. Doesn't work well, but might be useful.
DirectX Tutorials to understand underlying code
Good starting tutorial for DirectX. Really starts with the basics.
One of the best tutorials because it's so extensive. Goes into shadow mapping, and projective textures.
Excellent HLSL tutorial. You don't get any assembly here, but this is written like a text book and is much easier to understand than most.
Nice HLSL tutorial, more clearly written than a lot.
Good refresher on transformation matrices and the math involved. You don't really need to know the math, but reviewing this makes it easier to spot transformations.
Another excellent description of the projection matrix and how the transform math works to get an image on the screen.
DirectX11 Tutorial, but still applies to DX9. Good descriptions of different lighting effects and how textures work. The LightMaps was particularly helpful.
Interesting mix of HighLevelShaderLanguage and the asm versions.
Examples and discussions of advanced fixes
Mana84 comment for setting up the InverseMatrix feature in the ini file.
mike_ar69 question and Helix response about how to use surface creation mode feature, to fix some shadow maps.
Helix adding some details on using the new feature to add presets to autofixed shaders. This can allow automatic preset changes when menus come up or for cutscenes.
mike_ar69 giving some tips on how to fix shadows by using inverse matrix, and a little later an example fix using that technique.
DarkStarSword giving us some great detail on the different coordinate spaces, and how to apply a shadow fix.