I'm a heavy command line user (I don't have a graphical file explorer/manager for instance). Here is my top 42, in order of usage:

    ls, cd, git, ssh, make, e, cat, veille, rm,
    wpa_supplicant, grep, evince, mv, x, dhclient,
    cp, echo, todo, mplayer, scp, man, mkdir, ack,
    pdflatex, apt-get, apt-cache, sed, less, feh,
    racket, gcc, wget, xrandr, bg, svn, pmount,
    for, gpg, halt, ping, tail, top.

"e" is an alias for emacsclient ; "veille" is a script which toggles between "xset s 5" and "xset s default" ; "x" is an alias for "xinit" ; "todo" is a script which manage a text file which I use as a todo list.

"ls", "cd", and "git" are far more used than any other commands : 14808, 13256 and 10078 times respectively, against 3919 times for "ssh" which is just behind.

I obtained these data from my .bash_history. Here are the place of the commands that are listed in the article :

    "tr" is 76th
    "sort" is 66th
    "uniq" is 120th
    "split" is there only one time like many other command so its rank is not relevant
    Substitutions operations are what most "for" do so it is in my top 42. However see (1) below about the article.
    Files size are a mix of "ls" for individual file and "du" for multiple files, "du" is 65th
    "df" is 63rd
    "dd" is 473rd
    "zip" is 123rd (and funnily "gzip" is 122nd)
    I didn't use "hexdump"

(1) About the following line

    for i in *.mp4; do ffmpeg -i "$i" "${i/.mp4}.mp3"; done

I have two remarks. First, using the "-vn" of ffmpeg would accelerate the conversion by making ffmpeg ignore the video entirely. Second, substituting with '/' in the Bash expansion is not the right way to do that. "${i/.mp4}" would be "$i" without the first occurence of ".mp4". It is '%' that you want to use here.