I've noticed several other people showing their most frequently used shell commands so here it is from a few of my systems.

One of my spamtraps that publishes all the data to a webpage at http://www.spameatingmonkey.net :

selfishman@spamtrap:~$ history|awk '{a[$2]++} END{for(i in a){printf "%5d\t%s \n",a[i],i}}'|sort -rn|head
137   vi
46   ls
39   exit
29   /etc/init.d/qpsmtpd
27   cd
25   dig
23   tail
23   sudo
16   mysql
13   ps


The system that creates the SEM fresh domains list:

selfishman@spammonkey2:~$ history|awk '{a[$2]++} END{for(i in a){printf "%5d\t%s \n",a[i],i}}'|sort -rn|head
109   vi
85   ls
35   dig
23   screen
23   rm
20   ./prep-name-zone.pl
17   cd
14   exit
13   cp
10   ./test.sh


Finally, my primary testing and development system:

selfishman@rabidmonkey1:~$ history|awk '{a[$2]++} END{for(i in a){printf "%5d\t%s \n",a[i],i}}'|sort -rn|head
72   ls
60   vi
49   time
40   cd
34   exit
29   sudo
24   cat
17   ./john
13   gcc
12   crontab


I don't remember running JTR that often!