The main startup scripts are usually in /etc/init.d
Which scripts are called during startup depends on the runlevel (ie. whether you're starting up with a console or GUI, or some other arrangement). Different distributions often have their own 'user-friendly' methods for adding to the startup scripts, because runlevels can get rather confusing.
It's probably a good idea to use your distro's own method for adding a startup-script; if you try to do it yourself, it might not work (or might go wrong).
A busybox-based system (easily set up from scratch) dispenses with runlevels altogether and has a simple initscript: /etc/init.d/rcS
The Linux/Unix file structure actually makes a lot of sense. Don't forget, it's multi-user - if the Amiga was ever like this, you'd inevitably see something similar.
More details at:
http://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard