i agree that h264 is rather too slow for general purposes, plus it needs a lot of processor power for playback, specially on high-res movies.. i'd only consider it for web transmissions, and even then i wouldnt do it directly out of shake.
personally i use qt with jpeg a lot.. it's fast, plays on old machines, doesnt do intraframe compression (which i consider problematic for judging sfx shots) and is compatible with almost everything.
only annoying thing is that it seems to change gamma slightly, but that's true with most other qt codecs as well (sorensen etc). the solution (well, kinda, if somebody has a better idea i'd be keen to hear it) i to put a gamma
correction just before the proxy file-out node.
for the final render it really depends what your final output is going to be, and how much time/space you've got to waste....
for filmout, 16bit linear/10bit log image sequences are the way to go. for HDTV you'll want one of the video codecs (10bit 4:2:2 uncompressed on HDCAM SR, 8bit 4:2:2 uncompressed on HDCAM, DVCPRO HD for a DVCPRO tape etc)
++ christoph ++