Personally I use a shell script to do it automatically for me... with "file":

    #!/bin/bash
    # Usage: fix-extensions <media file(s)>
    # Renames the files to consistent file extensions based on content

    for file in "$@"; do
        [ -f "$file" ] || continue
        dir=$(dirname "$file")
        name=$(basename "$file")
        prefix="${name%.*}"
        ext="${name##*.}"

        magic=$(file -b "$file")
        newext=""
        case "$magic" in
        *"Apple QuickTime movie"*)        newext=mov;;
        "ISO Media, Apple iTunes Video"*) newext=mp4;;
        "ISO Media, MP4"*)                newext=mp4;;
        "ISO Media, MPEG-4 (.MP4)"*)      newext=mp4;;
        "Macromedia Flash data"*)         newext=swf;;
        "Macromedia Flash Video")         newext=flv;;
        "Matroska data")                  newext=mkv;;
        "Microsoft ASF"*)                 newext=wmv;;
        "MPEG sequence"*)                 newext=mpeg;;
        "Ogg data, OGM video"*)           newext=ogm;;
        "RealMedia file")                 newext=rm;;
        "RIFF "*" data, AVI,"*)           newext=avi;;
        "WebM")                           newext=webm;;
        esac

        if [ -z "$newext" ]; then
            echo >&2 "$file: not renaming, unknown extension for type '$magic'"
        elif [ "$ext" != "$newext" ]; then
            mv -v "$file" "$dir/$prefix.$newext"
        fi
    done