Hi Daniel, I use the method below... Not sure if it's the most efficient way, but it works for me.
I hope it helps.
To restore alpha transparency to a .tga using PS CS2 ~
1: Duplicate the layer (then hide the original/background layer)
2: Go to channels tab of the layer palette, and check "show" the Alpha 1 channel
3: Ctrl-click on that channels icon window and then Select Inverse (shift+Ctrl+I)
4: Now "hide" the Alpha 1 channel again.. and return to the layers tab (the opaque areas should be outlined by "marching ants")
5: Be sure the duplicate layer is active (blue) and hit Ctrl+X... the opaque areas should now be 100% transparent.
(Or you could just open the .tga with GIMP... Transparency seems to work there for some reason!?!)
Marie.