How/what software was used to create PBR textures in the 2000s? For example, Iron Man. The reflective metal is something I've always been curious on how it was done for the time period.
Another example is the older GTA's and Half-Life's.
How do these textures look so real on the colormap alone?

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In the case of iron man, its probably just raytraced reflections.
reflections back then and still for mobile stuff are based on fake cubemap that gets interpolated with texture, this cubemap is just environment being captured within engine or you make a fake texture. I made simple texture and blended with shader to get bubble reflection effect in Unity.
Textures were either handmade in PS or photosourced and adjusted to be straight / flat and went through highpass to remove lighting info. Then turned into greyscale with value adjustments for specular highlights and bump mapping.
In the early 2000s GPUs didn't have enough VRAM for baked normal maps, and didn't have enough zoomies to run more than 1 simple shader calculation per pixel. When you did see normal maps, it was only as tiny tileable detail normal maps that would help sell the effect of sand, rock or brick. (see halo 1)
So a model really only had a single texture, which depending on the artist would either be entirely hand-painted, sourced from images or a mix.
Then a simple light would provide a bland lighting effect and environmental coloring.
Things like AO, shadows and reflections were painted into the texture. There were many methods, but what I did was create tileable detail textures for each material, and blend them on top of a base lightness/color layer in PS.
Using dodge and burn tool in photoshop, I'd create the reflections and shadows. Baked AO (if available) would be set to multiply.
For dirt and rust I'd source it from a picture of something white and blend
For dust I'd take pictures of dirty black cars with MY HANDHELD DIGITAL CAMERA.
Scratches I liked to do with a mix of custom brushes and stencils I made, got from others, or pirated third party grunge brushes, which were an actual thing you could buy with real money.
To give you an idea of what the process would look like, here's a couple of before, during and after pics of me revisiting a skin I was never really happy with.
http://skins.thanez.net/oldschool/aks74u/1.jpg
http://skins.thanez.net/oldschool/aks74u/2.jpg
http://skins.thanez.net/oldschool/aks74u/3.jpg
http://skins.thanez.net/oldschool/aks74u/render.jpg
Unreal Tournament baked lighting info on the base texture to have that distint look.
Below is an example, using the same old 2k technique I baked lighting on the texture itself (3ds max, Mental Ray) using a plugin called Flat Iron. This saved ton on performance for VR.
The idea of baking is ancient. I recall people used Lightwave and Brazil render for 3d max in late 90th or something . Long before Render-to texture dialogs appeared in 3dmax . It followed an idea of "baking camera" using surface normals and UV space for ray tracing. Or just baking shader into UV including reflections.
they would normally used in conjunction photographic reference. the strange thing is they were pretty big images for
the texture limits of the day 2048 * 2048 so they can still be used in a 4k world, well almost
I had tried my hand at it but my PC wasn't fast enough to render even a million tris. I was poor and on a laptop my sister gave me. If I remember correctly, it didn't have a GPU, not even an integrated one.
I did use max 8 to bake lighting for reference and environment coloration to blend into my diffuse texture.