I just have too much time messing around...

 So...
You can now customize your color. Still not satisfied and want to customize the 
size of your Ink Pen?
The registry value is...
HKCU\Software\Microsoft\MSNMessenger\PerPassportSettings\(Your passport ID) -> 
InkPenSize
Yep, it's still a binary.
If you want to have an ultra-slim pen, just set it 
01 00 00 00. The larger the number is, the wider your pen will be.
The number goes like this:
01 00 00 00
02 00 00 00
...
...
ff 00 00 00
00 01 00 00
01 01 00 00
...
...
ff 01 00 00
00 02 00 00
01 02 00 00
...
...
et cetera.
I myself have tried, and, you have a 1-cm-wide (I mean, it's comparatively large) pen when the registry key is set 
00 04 00 00. Don't try to set it like 
00 ff 00 00...you'll get unforeseen troubles
