For ease I think ill seperate the Muxes from the flags.

Rendermode
==================================
Use SetGeometryMode(Texture, Z, shade, smoothshade, fog) unless otherwise stated
*************************************************************************
*   WARNING!								*
* 1 Cycle mode MUST copy to BOTH mux in Rendermode AND Combiner.	*
* Failure to do so will crash the RSP					*
* e.g.  Mux1	CLR_FOG*A_SHADE + CLR_IN*1-A 				*
* 	Mux2	CLR_FOG*A_SHADE + CLR_IN*1-A				*
*************************************************************************

MUX

Fog		CLR_FOG*A_SHADE + CLR_IN*1-A
		CLR_IN *A_SHADE + CLR_MEM*1-A

Fogless		CLR_IN *A_SHADE + CLR_IN*1-A	// If also ClearGeometryMode(FOG) 
		CLR_IN *A_SHADE + CLR_MEM*1-A	// Will allow vert Alpha. Remember to set again after

FadeAway	CLR_MEM*A_SHADE + CLR_IN*1-A	//Fades to invisible with distance, very cool
		CLR_IN *A_IN + CLR_MEM*1-A

1C FadeAway	CLR_MEM*A_IN + CLR_IN*1-A	//Special Combiner, very cool



Flags

A Transparent mode is required for ANY Alpha Register, including Texture Alpha.

AA ZBuffered Opaque		AA_EN, Z_CMP, Z_UPD, IM_RD, A_CVG, CLAMP, OPA

AA ZBuffered Interpenetrated	AA_EN, Z_CMP, Z_UPD, IM_RD, A_CVG, CLAMP, INTER	//Use if intersections are pixleated

AA ZBuffered Transparent	AA_EN, Z_CMP, Z_UPD, IM_RD, CVG*A, WRAP, XLU

AA ZBuffered Decal (OPA)	AA_EN, Z_CMP, WRAP, DECAL

Decal Transparent Texture	FC_BL IM_RD, FULL, DECAL	//Transparent Textures

AA Opaque			AA_EN, IM_RD, A_CVG, CLAMP, OPA		//Use Pre-Ordering

AA Interpenetrated		AA_EN, IM_RD, A_CVG, CLAMP, INTER	//Use if intersections are pixleated

AA Transparent			AA_EN, IM_RD, CVG*A, WRAP, XLU


1C FOG ZBuffered Opaque 	Z_CMP, Z_UPD, FC_BL WRAP, OPA	// No AA (Internal AA cool)

1C FOG AA ZBuffered Opaque 	AA_EN, Z_CMP, Z_UPD, IM_RD, FC_BL WRAP, OPA	//AA YAY

1C AA ZBuffered Transparent	Z_CMP, Z_UPD, IM_RD, FC_BL, WRAP, XLU // Can be used with 1C FadeAway



Combiner
===================================
First Cycle is normally 
TRILERP CC (Tex1 - Tex0) * LOD_Frac + Tex0 | AC (Tex1 - Tex0) * LOD_Frac + Tex0

Normally these are all 2nd cycle (Apart from 1C Fadeaway) but they will work with 1 cycle too, Replace Comb with Tex0 and Copy to 2nd mux.

Untextured 		CC (0 - 0) * 0 + Shade | AC (0 - 0) * 0 + Shade

Normal Texture 		CC (Comb - 0) * Shade + 0 | AC (0 - 0) * 0 + 1

Brighten Texture	CC (Shade - Comb) * Shade + Comb | AC (0 - 0) * 0 + 1


Transparent Types

By Default I have set EnvColour_Alpha to FF

Normal Texture 		CC (Comb - 0) * Shade + 0 | AC (Comb - 0) * Env + 0

Brighten Texture	CC (Shade - Comb) * Shade + Comb | AC (Comb - 0) * Env + 0

Transparent Texture 	CC (Comb - 0) * Shade + 0 | AC (Comb - 0) * Env + 0

WireFrame Texture 	CC (Comb - 0) * Shade + 0 | AC (Comb - 0) * Env + Tex0

1C FadeAway		CC (0 - 0) * 0 + Shade | AC (1 - 0) * Env + Shade



Special Modes
=====================================

Heat Distortion (Blurr Texture Edge)
Transparent Texture + AlphaCompare(Dither)


Flies/Partical System

EnvColour_Alpha = 20
AlphaCompare(Dither)
CC (Tex0 - 0) * Shade + 0 | AC (Tex0 - Shade) * Env + 0