DON'T USE TIF!! Gahh! /endspaz
TIF has no standard specification, so each program can interpret the data differently. TGA is much better, as it's still capable of RGBA and compression, and is handled by each application the exact same way.
Some programs will set alpha pixels to white, some to black, some to green, etc. It all depends. What you need to do is use a compositing application, such as after effects. That will solve many of the questions stated here.
I can't get After Effects though (not up for it, buying or downloading it cracked). Ok then TGA. That reminds me of this very old game, Carnivores, which used TGA as images. That's pretty much the only thing I've noticed TGA being used.