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Import the files as an image sequence using File --> Import, drag&drop it onto the Render Queue. Select the output module settings and choose Quicktime as your target format. In the Options select the Codec you will need. Choose an output directory, close the dialog, hit Render. If you're doing this frequently, consider automating things with a script or use Adobe Media Encoder. For more detailed info, check the online help system and tutorials linked from there.
You can set up a post-render action to take the image sequence as input and export it as a movie. See the "Use a post-render action" section of After Effects Help for more information. Answer back here if that page doesn't tell you what you need to know.
Also note you can import Image Sequences into Quicktime Pro and export them in other formats.
Got it. Thanks for the help! I appreciate it.