The last few times I had to restart my server, my iptables file was never saved and I had to load it from the backup. I always issue /etc/init.d/iptables save after any changes but for some reason it loads the default iptables file that came with the server.

Any ideas on what to change?

I would also like to use a default boot file that starts or restarts services like squid, nscd, postfix, iptables, etc - where can I edit that?

man iptables says "SEE ALSO: iptables-save iptables-restore"
so I think /etc/init.d/iptables save is maybe not the way to do it (which is why it does not work).

I am not acquainted with Centos but you need to google for system services centos which I just did, and found this

I have created an executable file called rc.defaultservices in the /etc/rc.d folder

How does that look?
I assume anything beginning rc. in that folder will get picked up on reboot?

No. Sorry but you are not doing this the "right" way.
Ugly hacks are OK (it's your machine), but it is better to follow the agreed "right way" (even though this changes all the time )

If you read the files in /etc/rc.d you'll see they are all shell scripts relating to services that expect an argument like start stop or restart
What they then do depends on the argument they are passed.

In /etc/ you'll see rc0.d rc1.d ... rc6.d rcS.d
rcS.d is for "Single user" or "Rescue mode". The other numbers refer to "runlevels"

Within these rcX.d directories are (or are not) symbolic links to the files in /etc/rc.d/
Whether there is a link or not, depends on whether you want a particular service to start or stop in that runlevel.

Runlevel 0 is generally halt
Runlevel 3 or 5 is generally "Run X and a GUI" (it very much depends on your distro)
The other levels are even more distro-dependant.

You could make all these symlinks yourself. It might take you some time.

Better is to read the link I gave you in the post above and learn to use either a GUI application to help you, or the CLI:
That means that squid will be started at boot for runlevels 3, 4 and 5

You need to do a bit more homework, then it'll all become clear.
"Allll right! I get it now, it's a sensible system".

Have fun. report back.