With one exception my preference is for transparent/translucent coloured folders. 

My 'tickler file' colour system is essentially traffic light based - RED things I have on hold/wait - typically a project which has been progressed to a final draft itinerary but the event is in two months time; AMBER for things in progress/awaiting responses from ANO - typically awaiting a receipt to file an expenses claim; GREEN for current action items - typically a set of meeting papers or itinerary for the next 24 hours.

In addition I use purple and emerald green envelope type folders for longer term projects - I do a lot of work which isn't suited to filing in ring binders - which I am not a big fan of anyway!

The only time I use manila folders is to circulate a greetings card for signature - because it is not transparent and it is really so inconspicuous around the office on each desk in turn.