In no particular order, here are things I've learned. As new things pop up I will update this post.
The current version of C4D that I am using is R21. In 2006 when I reworked the game assets, the then current version was R11. Fun fact - R21 cannot read R11's files. But all is not lost - R15 can read R11's files, and R21 can read R15's files. Every time I need to open up the old work, I have to use R15 as a go-between.
When you open an R11 file in R21 via R15, there are things to watch out for. An obvious one is the change in colour space handling. R21 uses linear work flow, and the sRGB colour profile. So you will need to check the Project Settings to be sure those are selected. R21 also has different controls for extrusion caps, and of course the reflectance and Physical Renderer is completely different. Fortunately most of these are easy to adjust. One hidden 'gotcha' is the different way group scaling is handled. In R11 if you had a group of objects and scaled them 200%, the topmost element of the group would have that scale as an attribute, which would affect all members of that group. Scale is kind of important as it modifies how textures are scaled and applied to objects, and it also affects things like the width of bevels and size of extrusions, etc. When I open up an old file in R21, this behaviour is retained. But I wanted to have everything normalized to a scale of 1, just to make sure everything behaved exactly as I expected. The trouble is that the adjustment would cascade through the hierarchy of a group - If a group was previously set to a scale of 2.56, and I reset that to 1, then all of its child objects would jump from a scale of 1 to a scale of 2.56, and so on, till I had chased all the scaling through to the bottom of the hierarchy. Then I would have to fix the bevels and extrusions to fit with the new scale property. Turns out, this is unnecessary. To fix the behaviour, all you need to do is copy the group to a new fresh R21 document, and then you can set the scale of the topmost element of the group, and all the child elements will automatically adjust - retaining their apparent size, but also retaining their original scale properties. Very quick way to clean up an old file.
When you render something out of C4D to use in a game engine like Aleph One, it will have a linear colour space applied. This is bad, because the resulting image will appear be far too bright. For colour images this means textures will be washed out looking, and normal maps will be skewed in a upper right direction. Photoshop hides this from you, because it understands linear colour space. But the game engine does not. And if you try to remove the linear colour space profile, Photoshop will alter the appearance of the image, which is NOT what you want to happen. You want the RGB values to remain exactly as they appear to be, regardless of how they were stored in the file. Fortunately there is an easy fix. In Photoshop, convert the image to 32 bits per channel colour mode, then immediately convert back to 8 bits per channel mode, choosing the 'Exposure and Gamma' method. Finally, you can go to the Edit menu, and in 'Assign Profile' chose 'Don't Color Manage This Document'. This will invisibly remove the Linear Space profile, leaving your image the way you saw it when developing it in C4D.
Don't think you can avoid the hassle of dealing with Linear Colour space by just turning that option off in C4D. That would be very frustrating for you. In linear work flow, changing a light value from 100% to 200% will result in twice as much light being emitted. Makes sense, right? Without linear work flow, that amount of change in a light will be imperceptible. You will routinely end up cranking lights up to values in the thousands just to try to get the results you want. So do yourself a favour and always have linear workflow enabled.
That's all for now. I will add more as things occur to me.