Here is a answer I wrote a week agoa that might be helpful.
Best,
Andrew
With all of the many render settings, I get asked what is the best way to render in After Effects. Well there are many things to consider. Is the video being rendered over a network? If so each computer must pick one frame to render at a time and thus you cannot use a single file formate like AVI or MOV. Instead image sequences like PNG or TIFF are ideal because of the uncompressed image data. For the average Joe F. Ex, the single file rendering is a great solution.
The render option I recommend is a QuickTime Movie. When you setup your output module, choose Quicktime for the format and then for the codec, here are the three I recommend. I rendered a minute of video with the 3 formats.
1. PhotoJPG (at 95% quality)
* Smaller file size
* Fast compression
* Withstands several generations before losing apparent quality
* 239 MBs for 1 minute video @ 864