After Effects uses the Adobe Media Encoder to encode most movie formats through the Render Queue panel. You can use QuickTime to encode other movie formats (such as raw DV streams) through the File > Export menu.
For most output formats, you can specify format-specific encoding and compression options. In many cases, a dialog box opens and presents these options when you choose a format to export to, either in the Output Module Settings dialog box or from the File > Export menu.
Formats encoded by the Adobe Media Encoder share a similar export settings dialog box, which you can open by clicking the Format Options button in the Output Module Settings dialog box.