Disabling first via CCM - this does not stop anything - it simply allows current processes to complete and disallows any new requests.
Typical for a place where you don’t have a maint window and cannot determine if everyone has indeed logged off.
I know that you can check if there are any users logged on via the CMC - but i think I had issues with that info.
Tomcat admin is probably more trustworthy - but it’s the idle users that tend to catch one and here it depends on how you set your idle time outs etc.
The DISABLE suggestion was initiated at a time when XI was pretty new and it was almost impossible to identify and possible repair unsyched entries in the FRS(s) and the CMS. I heard that was resolved.
NOTE: CMS has to be running for the enable / disable function.
As to stopping things - one would assume that it’s a logical top down and bottom up process i.e dependancies / core applications / web&application servers. And if you look at the dependancies on the services - there are almost none - Event Log being the common factor for all.
I then think one has to consider monitoring and logging - as certain instances could trigger events or alarms - depending on your internal monitoring methods.
And not to forget that there are is some periodic system cycling occuring on certain XI servers - I’ve never had an issue with this, but it’s worth keeping in mind if wanting a clean shut down - check your logs to see if you ever interrupt these processes when having strange behaviour.
But yeah, for a relatively clean process:
Shutting Down:
Disable everything except the CMS
Stop everything except the CMS.
Stop the CMS
Stop Tomcat.
Reboot
Starting up:
Tomcat
CMS
FRS(s)
Everything else …
…And I can’t recall if restarting then resets the disabled status … 
But - last I heard, one could not automate the disabling / enabling part …
There is no need to delay by 30 minutes - you could probably get away with about 5 to 10 minutes - and can re-issue stop commands but not start commands.
But we all have our own opinions and experiences, so make sure you read up anything you can on this:
… And keep in mind that XI 3.0 only displays Tomcat and SIA in the CCM window and you have to click on Manage Servers to see the list, so maybe don’t spend too much time on AI type automation scripts etc 
MikeD 
(BOB member since 2002-06-18)