File format suggestions

Hello!
I started working in the business of videomaking about two years ago, and under all this time we have always used Quicktime Motion JPEG-B as our main video container. Motion JPEG-B offers very high quality but is much smaller than "animation" which is almost lossless. However, the latest quicktime updates have flagged Motion JPEG-B as an "older codec" which gets me to think that there is a new better codec, that should replace MJPGB in every way (or else there would be no reason to hide the codec at default and call it an older codec). The only codec that I can think of that could be better is h.264. It's a bit trickier to configure to get exactly the right quality (not too low, not too high) but seems to have the same or even better quality at smaller sizes and it also is playable by anyone with quicktime installed. (If you for example consider to use divx as codec you have to count in that only computers with that codec installed can play it, and it's far more commmon to have quicktime than divx installed.)
So, can I get some input on what codecs I should use and for what end? (webb, computers, broadcast, archiving source footage) for now we have to export all our shot footage from premiere to quicktime motion jpeg-b because after effects can't read sony ex-1 mxf clips. Needless to say we have to archive massive data on blu-ray because the footage gets so large in motion jpeg-b.
Thanks in advance!
/ Olle

We haven't upgraded to CS4 yet, we use CS3. My colleague has tried CS4 though and didn't get mxf to work anyway, but he only tested the program at a friends briefly. We use a Sony EX-1 with the redrock adapter.
To comment your answer uncompressed and animation is too large to be economic for us, microcosm and prores i have never heard of. Thus H.264 sounds like the most interesting format. The thing is that you want to use a format that is most like a standard. Is the h.264 going to be here for a while or soon replaced. Motion Jpeg-B i know A LOT of companies, freelancers and broadcast stations that use. But i really would like to change our default format to h.264 if it is reliable as we also have noticed certain issues with Motion Jpeg-b.
Thanks for your time Mylenium!
/ Olle

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