This is a huuuuuuuge question, and frequently asked.
Here is the very simple answer:
If you're encoding for final delivery, then you need to ask your client what they want.
If you're encoding for intermediate or archival purposes, then you should use a lossless codec. For 8-bpc work, I like QuickTime movies encoded with PNG or Animation, depending on the kind of imagery.
Here's a link to a section in After Effects Help about compression:
"Encoding and compression options for movies"
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Todd Kopriva, Adobe Systems Incorporated
putting the 'T' back in 'RTFM' :
After Effects Help on the Web
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