This is just a super quick list. You need a minimum of proficiency with Unix shells (bash and tcsh are the ones mostly used on the cluster) and Linux systems.

passwd Changes your user password.
  1. Type your old password
  2. Insert new password
  3. Confirm new password
ls Lists folders and files in current directory
mkdir Create new directory into the current one

mkdir newdir

cd Changes directory.

Examples:
cd test (go to a directory named 'test')
cd .. (go to parent directory)
cd ~ (go to home directory; ~ is a short-cut for /home/username)
rm Removes specified file or directory

rm filename (remove single filename)
rm *.txt (remove ALL .txt files into current directory)
rm -r dirname (remove directory and all the files it contains)

Please be careful when you use the -f option! :-)

rmdir Removes specified EMPTY directory

rmdir dirname
pwd Prints current absolute path
man Shows specified command's manual page

man ls (shows ls help)
vi x.sh VI is a text editor. If x.sh does not exists, vi creates a new file called x.sh and opens it;

otherwise, it just opens the existing file.
less textfile less is a text pager. Opens textfile in read-only mode. You can use up and down arrows to move across the text. It shares many commands with VI.
chmod Changes POSIX permissions of a file or directory. Allows to protect files from unwanted access.

r :read permission
w :write permission
x :exec permission

chmod +x file.sh (allows execution)
chmod -w file.sh (denies write)
chown Changes owner of a file or directory

chown username file.sh

top Shows current executing processes
cat Prints the content of a file on screen
grep Filters the content of a file by outputting those lines which contain the specified pattern.

grep pattern file.sh
You can exploit piping to filter the output of another command with grep:
cat file.sh |grep home
cat file.sh |grep "home page"



Further information on Linux shell can be found here:
Useful Linux Commands for Newbies - www.tecmint.com
Shell Redirection - Wikipedia
20 Advanced Commands for Middle Level Linux Users - www.tecmint.com