There are 2 places I use when I need to add "run-once" commands:

Once at every user login (be it Graphical/GDM or text/console login): ~/.profile

Pros:

• It works even if no GDM/X11/Graphical server is used. Meaning it will work with SSH and text-mode logins


• It is NOT evaluated when a gnome terminal starts, as required. ONLY at login


• Executed with user priveleges, its secure while allowing full access to personal scripts.


• Run after all mounts are done, so the whole filesystem is avaliable.

Cons:

• If a user logs in, logs out and logs in again, it will be executed again, once per login. So its not a "true" system start up only. But it may suit your need.


• Since this is executed even in text-mode logins, its advisable NOT to place any command that requires a GDM/X11 server (like synergy daemon)


• Bash is only used with text-mode logins. So if using GDM, no bashisms are accepted in the script, since Ubuntu will run it with dash

Once when GDM starts (before any user logs in): /etc/gdm/Init/Default

Pros:

• Executed only once, no matter how many users log in or out


• Can be used for both text and graphical commands


• Run after all mounts are done, so the whole filesystem is avaliable.

Cons:

• Run using gdm user. So personal scripts and path to them must be world-readable and executable


• Cannot be used if no GDM server is used (duh). So it wont run in text-mode start-ups


• Again, not run in bash, so bashisms must be avoided.

Use the method that suits your need.