lossless animation or uncompressed 10bit are very good options but they require a lot of drive space if you're using hd.
quicktime png is lossless and uses less drive space, but does require a bit more processing power when using it in ae. not much of a problem if you're working with one or two clips in a comp, but if you are compositing several, it will effect performance.
if you are working in prores, then later versions of windows quicktime can read prores, so that could be an option.
quicktime photo-jpeg is also very good, and windows quicktime can read/write that codec.
avid offers several of their quicktime codecs for free, so those are options. their dnxhd is about the same as prores, and would be a good option for hd.
You can use either QT's Animation or PNG codecs; at best quality, both are lossless and both support alpha channels. Of the two, I'd select PNG for the smaller file sizes.
The exception: if I'm making something that has a lot of transparent background in AE, like an animated lower-third, I'd go with Animation because of the way it encodes; the files size would be MUCH smaller than PNG in this instance.
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