Where and how are logon and startup scripts for graphics desktop managed?

Question

Where and how are the Ubuntu equivalent of your personal Windows configuration stored? Something akin to HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run as well as the Start Up menu.

I have spotted the System | Preferences | Startup Applications menu entry which seems to do some of it, but it doesn't appear to cover most of the things.

I am more concerned with those which a pertinent to a graphics login, either directly at the computer or remotely through NX or x2go for instance, as well as those that apply to every user such as this xrandr and those the user might configure personally

For instance I have got an xrandr script to set my screen resolution and I also need to configure Firefox to allow me to use multiple profiles. Currently I do all from the gnome terminal after logging onto the desktop.

Is there some guide where I can configure all these settings at logon time? The main thing is the should only apply to logging to Ubuntu or Gnome destkop, not logging on at the console.