When using the command line it is important to realize that the command line follows a basic syntax, which every command follows. That syntax is
command [options] [arguments]
Each line you type on the command line will begin with the name of the command itself. These commands can be short and terse like ls or cd, or longer and more descriptive like traceroute or mysqlcheck. However you always start by giving the command that you want to run.

The older commands from Unix's tend to be short, often obscure strings of letters and numbers like chmod or ps4pdf. This was done to save on typing speed, as in the old days when Unix was first created the only people who would be the systems administrators and operators. All of whom would be expected to know the system and its commands inside-out. As time progressed the commands have become more descriptive, making it easier for someone to deduce what the command is supposed to do (eg mysqlcheck is used to check the tables in a mysql database for corruption).

Options are used to change the way the command does its job. They are denoted using a dash, '-', or double dash, '--', and will proceed any arguments the command takes. Options often change the way the output of the command is displayed. For instance using the -l option for the ls command will cause the command to display additional info as part of the directory listing.
-bash-3.00# ls 
aquota.group  boot          dev        hacked_ips  media            opt           quota.group  sbin     srv          tmp
aquota.user   cert-default  etc        home        mnt              phishing.zip  quota.user   scripts  stunnel.rnd  usr
bin           cert-sensoro  hack_list  lib         mysqlaccess.log  proc          root         selinux  sys          var
-bash-3.00# ls -l
total 200
lrwxrwxrwx     1 root root      39 Jul 13 12:10 aquota.group -> /proc/vz/vzaquota/0000009f/aquota.group
lrwxrwxrwx     1 root root      38 Jul 13 12:10 aquota.user -> /proc/vz/vzaquota/0000009f/aquota.user
drwxr-xr-x     2 root root    4096 Jun 17  2006 bin
drwxr-xr-x     2 root root    4096 May 22  2005 boot
-rw-r--r--     1 root root     911 Dec  8  2006 cert-default
-rw-r--r--     1 root root     886 Dec  8  2006 cert-sensoro
drwxr-xr-x     2 root root    4096 Jul 13 12:10 dev
drwxr-xr-x    58 root root    8192 Aug 30 01:00 etc
-rw-r--r--     1 root root    2500 Jun  6 11:12 hack_list
-rw-r--r--     1 root root     411 Jun  6 11:13 hacked_ips
drwx--x--x     8 root root    4096 Aug  9 23:29 home
drwxr-xr-x     8 root root    4096 Nov 27  2006 lib
drwxr-xr-x     2 root root    4096 May 22  2005 media
drwxr-xr-x     2 root root    4096 May 22  2005 mnt
-rw-r--r--     1 root root       0 Apr 17 16:33 mysqlaccess.log
drwxr-xr-x     2 root root    4096 May 22  2005 opt
-rw-r--r--     1 root root    1791 Jul 30 14:36 phishing.zip
dr-xr-xr-x  3206 root root       0 Jul 13 12:10 proc
-rw-------     1 root root 1024192 Sep 27  2006 quota.group
-rw-------     1 root root 1278656 Sep 27  2006 quota.user
drwxr-x---    13 root root    4096 Aug 29 23:29 root
drwxr-xr-x     2 root root    4096 Jun  3  2006 sbin
drwxr-xr-x     5 root root   12288 Aug 29 23:27 scripts
drwxr-xr-x     2 root root    4096 May 22  2005 selinux
drwxr-xr-x     2 root root    4096 May 22  2005 srv
-rw-------     1 root root    1024 Jun  3  2006 stunnel.rnd
drwxr-xr-x     2 root root    4096 May 22  2005 sys
drwxrwxrwt     3 root root    4096 Aug 29 23:28 tmp
drwxr-xr-x    16 root root    4096 Jul 13 12:11 usr
drwxr-xr-x    22 root root    4096 Jun 17 17:18 var
Options can be either long or short. Long options will start with a double dash, and are whole words. If there are multiple words in the option they will be separated by a single dash (eg the --line-numbers option for iptables). Short options will be a single letter, and can often be combined into a single set, so
ls -l -a -p -h
is equivalent to
ls -laph
There are a number of common options, that are shared among multiple commands. However one of the most useful to remember is the -h opton, which will usually give you a brief help message (its usage in commands like ls, du, and df are exceptions to this rule).

After any options will come the arguments to the command. Not all commands take arguments. Some commands do not take any arguments, some will have optional arguments, and others will require arguments. Commands that require arguments are often used to change or alter a file, and the filename is the the required argument. For example, the chown command changes the ownership of a file (DON'T use this command if you don't know understand the consequences of changing a files ownership), and requires two arguments, the username of the new owner, and the file to be modified. So to change the owner of a file named sales-Aug2007.doc in the current directory to the user mark, you'd enter
chown mark sales-Aug2007.doc

This is a very basic intro on understanding command line syntax, and there should be more to come.