How do you find exploits using the *NIX shell?
Check the active processes
Use the "ps" command to look for odd or unknown processes, if you aren't sure what to look for there, user "netstat -ae | grep irc" and/or "netstat -ea | grep 666" and look for ports 6666, 6667, 6668, 6669, these are common ports used for running IRC bots, they may have the name "irc" listed against them, or may have "httpd" or sometimes other regular services names.
Check your crontab and see if there is a strange entry, these are used in many exploits to restart IRC bots, even when admins or automated process monitors are used to kill a rogue process.
Check for hidden files or directories
Check for hidden files or directories you dont expect to see, those starting with "." (dots) and also look for ". " (dot, space) often favored to try and catch searches for hidden directories.
Other examples of searches that may help pin down exploits and/or unexpected files and folders:
find /home -type f | xargs grep -l MultiViews find . -type f | xargs grep -l base64_encode <<< this can produce false positives, it is valid in many mail/graphics scripts find . -type f | xargs grep -l error_reporting find / -name "[Bb]itch[xX]" find / -name "psy*" ls -lR | grep rwxrwxrwx > listing.txt