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When Emacs is started, it normally loads a Lisp program from the file .emacs or .emacs.el in your home directory. We call this file your init file because it specifies how to initialize Emacs for you. You can use the command line switch `-q' to prevent loading your init file, and `-u' (or `--user') to specify a different user's init file (see Entering Emacs).
There can also be a default init file, which is the library
named default.el, found via the standard search path for
libraries. The Emacs distribution contains no such library; your site
may create one for local customizations. If this library exists, it is
loaded whenever you start Emacs (except when you specify `-q').
But your init file, if any, is loaded first; if it sets
inhibit-default-init non-nil, then default is not
loaded.
Your site may also have a site startup file; this is named site-start.el, if it exists. Like default.el, Emacs finds this file via the standard search path for Lisp libraries. Emacs loads this library before it loads your init file. To inhibit loading of this library, use the option `-no-site-file'. See Initial Options.
You can place default.el and site-start.el in any of
the directories which Emacs searches for Lisp libraries. The variable
load-path (see Lisp Libraries) specifies these directories.
Many sites put these files in the site-lisp subdirectory of the
Emacs installation directory, typically
/usr/local/share/emacs/site-lisp.
If you have a large amount of code in your .emacs file, you should rename it to ~/.emacs.el, and byte-compile it. See Byte Compilation, for more information about compiling Emacs Lisp programs.
If you are going to write actual Emacs Lisp programs that go beyond minor customization, you should read the Emacs Lisp Reference Manual.