Within the same machine and a short time span, there's no difference in quality between a reference movie and a self contained quicktime movie. When playing it out on a different machine, a reference movie may not play at all.
A reference movie contains links to the source/render files. A self contained quicktime movie contains the video and everything needed to play.
Go AIC if you can, I recall Apple's white paper mention lower error rates on renders on AIC vs HDV.
Skip the H.264, if you can, if your playback machine is fast enough to play it back in real time, and you have sufficient hard disk space. You may need to have FCP/FCE installed to play back AIC/HDV, so do a check.
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