I'm not the author of any of these guides, but over the course of my own modding adventures, I have found them and compiled them. This was originally a post on tumblr. If you want to get in contact with me, send me an ask/message over tumblr at gyrkehim.
These aren't organized the best, sorry!
CLOTHING
7.0 Mashup Walkthrough by Khloris
A Blender Weight Transfer Technique by Felis
How to split legs for weighting by key
How to combine meshes seamlessly by bluberry
UPSCALING
M Middie Refit Walkthrough by Khloris
Yet Another Vanilla Upscaling Guide by Lighty
Upscaling Guide (Masc Bodies) by key
Upscaling Guide (Fem Bodies) by key
How to Upscale Vanilla Outfits by key
FTM Porting Guide by key
How to make a bulge by key
How to fix UVs/warped textures after upscaling by key
Upscale to Lux+ Redux by oneiroy
Upscale Guide by Quoth
HAIR
hair weights aren't scary and you are brave: an ffxiv modding guide to manually painting weights by lyss
Textured Hair Guide by belovedcrypt
Hairstyle mashup walkthrough by rasp
How to add hat compatibility by rasp
Custom Highlights by Felis
How To: Midlander to Highlander Hair "Ports" by Ellie
Hair Skeleton Porting Guide (+M!AuRa 1 to Fem 6) by khanter
How to use multiple hair skeletons for one mashup by sleepybnuuy
Hair porting guide (incl. to miqo'te) by vievinvalor
How to make hair holographic by Fii
FACE
Double chin sculpting tutorial by workingelezen
Adding catchlights by priestess
Porting sculpts from pre-DT to 7.0 by Eme
How to add extra toggles by Maja
How to make piercings for beginners by Yuna
AsymFaces - 3d Creator & DIY Guide by Spiswel
VFXEDITOR
vfx editing notes by taco
VFX Texture File Paths by (unknown)
Adding vfx to an item without one by ocealot
VFX, Texture, Model, Animation, and UI Guides on the vfxedit wiki
TEXTURES
How to make tattoos appear on all skin tones by TheTiredPopoto
7.0 face texturing guide by DVNO
Texture path generator by Yuria
Loose files guide by Yuria
How to make a tattoo glow by Alexstrasza
Deleting Baked Shadows in Vanilla Gear by Kirke
MISC
Anata’s Guide to IMC/Toggles on Penumbra by Anata
Gear Mod Packing & IMC Toggles by samson312
Colorsetting Guide by Khloris
Character Scroll Guide by Bacara
How to add and upload variants to Heliosphere by key
How to rig a mesh to a skeleton by key
Shape keys guide by bewearz
Baby modder introduction on modding101.net
Dawntrail shaders on old gear by JB
Reni's guide on Penumbra & Glamourer by Reni
Swapping one item onto another (also applies to hair) by Reni
Fixing "Forbidden File Redirection" Errors in Penumbra by funny lizar/peachy
These aren't organized the best, sorry!
CLOTHING
7.0 Mashup Walkthrough by Khloris
A Blender Weight Transfer Technique by Felis
How to split legs for weighting by key
How to combine meshes seamlessly by bluberry
UPSCALING
M Middie Refit Walkthrough by Khloris
Yet Another Vanilla Upscaling Guide by Lighty
Upscaling Guide (Masc Bodies) by key
Upscaling Guide (Fem Bodies) by key
How to Upscale Vanilla Outfits by key
FTM Porting Guide by key
How to make a bulge by key
How to fix UVs/warped textures after upscaling by key
Upscale to Lux+ Redux by oneiroy
Upscale Guide by Quoth
HAIR
hair weights aren't scary and you are brave: an ffxiv modding guide to manually painting weights by lyss
Textured Hair Guide by belovedcrypt
Hairstyle mashup walkthrough by rasp
How to add hat compatibility by rasp
Custom Highlights by Felis
How To: Midlander to Highlander Hair "Ports" by Ellie
Hair Skeleton Porting Guide (+M!AuRa 1 to Fem 6) by khanter
How to use multiple hair skeletons for one mashup by sleepybnuuy
Hair porting guide (incl. to miqo'te) by vievinvalor
How to make hair holographic by Fii
FACE
Double chin sculpting tutorial by workingelezen
Adding catchlights by priestess
Porting sculpts from pre-DT to 7.0 by Eme
How to add extra toggles by Maja
How to make piercings for beginners by Yuna
AsymFaces - 3d Creator & DIY Guide by Spiswel
VFXEDITOR
vfx editing notes by taco
VFX Texture File Paths by (unknown)
Adding vfx to an item without one by ocealot
VFX, Texture, Model, Animation, and UI Guides on the vfxedit wiki
TEXTURES
How to make tattoos appear on all skin tones by TheTiredPopoto
7.0 face texturing guide by DVNO
Texture path generator by Yuria
Loose files guide by Yuria
How to make a tattoo glow by Alexstrasza
Deleting Baked Shadows in Vanilla Gear by Kirke
MISC
Anata’s Guide to IMC/Toggles on Penumbra by Anata
Gear Mod Packing & IMC Toggles by samson312
Colorsetting Guide by Khloris
Character Scroll Guide by Bacara
How to add and upload variants to Heliosphere by key
How to rig a mesh to a skeleton by key
Shape keys guide by bewearz
Baby modder introduction on modding101.net
Dawntrail shaders on old gear by JB
Reni's guide on Penumbra & Glamourer by Reni
Swapping one item onto another (also applies to hair) by Reni
Fixing "Forbidden File Redirection" Errors in Penumbra by funny lizar/peachy