Shockwave.ibx and Shockwave.tsb:These are cache files, a FS-generated format used for storing the model itself.
Shockwave.pof:This is the actual model file.
shockwave3D-Glow_*.dds:We'll get back to that later.
shockwave.eff (Do you mean shockwave3D-Glow.eff or shockwave01.eff?):This is a FS-specific format which defines an animation, telling FS to use a certain number of files in a certain format, displayed at a certain FPS.
shockwave01_*.dds:These are most likely the files for the 2D shockwave effect (I don't have the MVPs here so I can't check), rendered as a sprite always facing you (so it's always a circle).
shockwave3D-Glow_*.dds:These are the files for the 3D shockwave effect, rendered as a model so it's seen at an angle.
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The 2D effect is the brighter one, and I'm assuming that's the one you want to change. Extract the files shockwave01_0000.dds through shockwave01_0095.dds from the VPs.
You'll need a Photoshop plugin to edit DDS files, and once you can read them, change the Hue/Sat/Lum or the Brightness/Contrast
by the same values for each DDS file so as to darken it a bit. (with these effects, which lack an alpha channel, brightness = opacity. it's an "additive" effect.) Batch processing could make this a bit quicker although I don't know how to do that in PS (GIMP ftw).
I also recommend saving the effects as TGA files, then using a program like ATI's Compressionator to convert back to DDS
using DXT1 compression.