Hi Adam,
Well as far as I've found there is no control over the strength of Peak/Waveform coloring, particularly when custom colored. I mentioned in the Pre-Release forum some time back (
http://forum.cockos.com/showpost.php...&postcount=44) that if any of the media waveform/peak tick options are selected (ticked) together with it's media background relative - Reaper still draws what default peak colors are set in the Theme editor and blends the Track/item/Take applied custom color together - which gives a somewhat poor waveform/peak coloring result (usually dull but may depend)...
So, even if for example you just select coloring for the Waveforms/Peaks - they seem to be nice and vivid but there's also afaik no control over the weight or strength of the coloring applied.
A related request was also put on the issue tracker by Reflected - but this was whilst it was still in Pre prior to the official 3.66 release:
http://forum.cockos.com/project.php?issueid=2793
Oh... you should know this thread (where the above links come from):
http://forum.cockos.com/showthread.php?t=62283
I guess everyone was quite busy with other pre-release matters at the time but - Schwa did an awesome fix on the waveform/peak highlight bug that was found - so it's a big improvement from how things were working before.
sorry for the length of this post...