Much of this has been taken from linux.org, although not everything on that site is releavant to what I’m interested in at the moment, it is still a good reference.

Directories

/bin – one of the most important directories in Linux! There’s a lot of commands/programs in there. Those in red or green are programs.
/etc – most of the Linux configuration files are here
/dev – system device directory
/lib - library directory, lots of programs refer to library files
/opt – this directory provides storage for large, static applications
/sbin – system program directory
/tmp – temp directory
/usr/local – for locally installed software
/var – directory for files that might change in size…

Commands

/usr/local/apache/bin/httpd -v — find out the version of apache
cd .. — Down a directory
cd /etc — Takes you directly to the directory
cp – copy
df – shows disk space usage
find – find files
grep – find text in files
gzip — compress/uncompress files, files will have .gx extension
ls — List
ls -a — List, including hidden files
ls -l — detailed directory information
ls a* — lists all files beginning with a
man — help
mkdir - make directory
mv – move
php -v – PP version
pwd – shows current working directory
rm — delete files
rmdir – delete directory
shutdown -r down — reboot
tar — zip/unzip, files will have .tar extension
whoami – who I am!

Help
man
command –help e.g. cp –help

Permissions
chmod is used to change permissions. Permissions are split into User | Group | Others. For each type of permission there is a number that specifies what can be done:

4 – read
2 – write
1 – execute

So an example would be… chmod 600 my_text_file.txt
I have read/write permissions (4 + 2), but everyone else has no permission to the file