Welche Version von AE? Welches System? Welche Ausgabe? Generell wird sowas in the Output Module Settings mit gespeichert und für die -zig vorgefertigten für H.264 & Co. ist Audio da eigentlich auch immer schon angeknipst. Für andere Sachen mußt du dir halt eventuell nur einfach so ein Setting erstellen und es immer benutzen. Ansonsten gibt's leider keinen automatisierten Weg sowas zu überprüfen oder zu erzwingen, weil AE sich nur die CoDecs und deren Einstellungen merkt, aber ansonsten keine systemübergreifenden Sachen...

Mylenium

Todd's suggestiion for creating templates is a good one.  Whenever rendering a movie file out of After Effects or Adobe Media Encoder, I almost always use custom templates or built in presets.

However, if you rendered to a production codec and don't want to rerender that comp from the beginning, you could probably reimport the file back into After Effects, add the audio, and do a quick rerender without any noticable loss of quality.  In the future, I would even suggest rendering to a high quality image sequence like TIFF or PNG and bringing them back into After Effects or an NLE like Premiere Pro to add back the audio.

Obviously, this is an extra step and it depends on what you need the files for, but one of the reasons I like using image sequences is because they're extremely high quality, and if the render is interrupted you can start it again from where you left off as long as you have "Skip Existing Files" selected.  This is especially usefully for really long render times, where your computer might be interrupted for whatever reason.

If you're rendering to a Quicktime and the render gets stopped, the file is useless and you have to rerender from the beginning.