Applications have to be written with PAM library support.
To get a list of the applications on your system that can use PAM in some way, type:
ldd /{,usr/}{bin,sbin}/* | grep -B 5 libpam | grep '^/'
returns:
/bin/login: /bin/su: /sbin/mkhomedir_helper: /sbin/pam_tally2: /usr/bin/chfn: /usr/bin/chsh: /usr/bin/passwd: /usr/sbin/atd: /usr/sbin/chpasswd: /usr/sbin/cron: /usr/sbin/newusers: /usr/sbin/sshd:
ldd $(which prog_name) | grep libpam
If it returns anything, then it can use PAM.