Toribash
A lot of users use the .tga format. Our system is set up so that it will convert to .tga in the end anyway though, so the key is uploading a format that has transparency in it.

.gif, .tga, and .png all have transparency, and you can use them to upload you texture.

my personal recommendation is that you use .tga if you have created and edited your own alpha channel, or .png if you are using a program and erasing away to get transparency (letting the program create the Alpha).