As part of my track texturing I normally draw a big bright arrow on my texture so that I get it all running in the correct direction.
The first colour I chose was pink (255, 0, 255)
When I coverted this .gif to a .pac and looked in buldozer I saw that the pink was not there and was in fact transparent. I went in game (1.94b) and the same was happening there.
Is there a performance hit compared to .paa's
Its a lot easier that buggering around with alpha channels. (unless you want a pink car then you are in trouble - and dirty glass I suppose)