The default startup files for the Terminal don't allow you to easily run applications from /usr/local/bin or ~/bin (Home /bin). To change this, and set up some other basic shell stuff, you need to change your user startup scripts. If any of these files already exist in your home folder (use ls -a in a new Terminal), use BBEdit or TextWrangler to add the quoted lines to the appropriate files. You only need to do this once.
Open a Terminal and type the following (in a new terminal you should be in your Home folder, stay there):
For bash (default shell starting with Mac OS 10.3) (fill in your login username in the PATH statement):
$ echo "export PATH=/Users/[your_user_name]/bin:/usr/local/bin:/usr/local/sbin:/usr/X11R6/bin:\$PATH" > .bash_profile
$ chmod 644 .bash_profile
For tcsh (the old default shell):
% echo "source /usr/share/tcsh/examples/rc" > .cshrc
% echo "source /usr/share/tcsh/examples/login" > .login
% echo "source /usr/share/tcsh/examples/logout" > .logout
% chmod 644 .cshrc .login .logout