Hmm…I am a little confused about the question. Are you asking what formats others are using in production? Or are you asking about quick time specifically? I think that the answer will very depending on what you are trying to accomplish and how you are getting your footage. Regardless though, it is probably not a good idea to compress your footage until final output if at all possible. So any format that will not compress your footage is probably a good choice.
As far as Quick time goes, if you get the pro version it gives you all kinds of options on how to export your video, including alphas. Also another application that I use a lot is Adobe Media Encoder. Anyway, hope this helps answer your question.