How can I convert AC3 audio files to AAC?
VideoLAN can do this. Select "Streaming/Transcoding Wizard" from the File menu. Choose "Transcode/Save to file". On the next page click "Choose" and open your AC3 file. On the next page tick "Transcode audio" and choose "MPEG 4 Audio" and choose the desired bitrate. Click "Next", choose "MPEG 4 / MP4", click "Next" again and "Choose..." where to save the file. "Next" and "Finish".

The file VideoLAN creates has the extension .mp4, change it to .m4a and there you go.