Do you want the script to run regardless of who is logging in, or do you want different (or no) scripts for different users?
If you want to have a general startup script for all users, you can insert the script into /etc/init.d, and then use chkconfig to enable it for the run levels you want it to run at.
chkconfig 3 boot.script on
this will enable the boot.script file in runlevel 3. It will create a symbolic link to the script in /etc/rc.d/rc3.d/ That way, whenever the computer enters runlevel 3, it should run. If you want user level scripting... it's definitely doable, but I'm not positive on how to do it for the command line.
Oh, and the chkconfig tool is redhat specific, so if you're using a different distro, you might have to do it manually, download chkconfig, or use a similar tool. I know gentoo, debian, and suse have similar functions, but with different names. Something like rc-update I think.
This post had something similar, it might be of interest.
OK... just talked to a friend fo mine about it, and there is an easier way for post login stuff to run in command line. In each user's home directory, there is a file called .bashrc or .cshrc depending on which shell you use. anything in that file will be run after that user logs in. That's probably your best bet....