How to take the web server offline for maintenance when its a single server

The way this is done for a lot of web apps is to create a flag file when the site is in maintenance mode. A file, which is normally included in all other page files, looks for that file and either sends the user to the main site or to a "this site is in maintenance mode" type of page if the flag does exist. Simply delete the flag file to restore the system to normal operation.

I would go with your third approach "We're offline" Site in IIS, say you named it Offline, if it has no host header specified it will serve all requests not picked up by any of the other sites which have a matching host header. To prevent this you just stop all other sites.

Assuming you have IIS Scripting installed, open an elevated PowerShell:

import-module webadministration

now you can stop all sites except the Offline one:

Get-ChildItem IIS:\Sites | Where {$_.Name -ne "Offline"} | Stop-WebSite

when the SQL-Server is back up, start them up again:

Get-ChildItem IIS:\Sites | Where {$_.Name -ne "Offline"} | Start-WebSite

If you have FTP sites as well, the commands will show an error because you can not pipe an FTP site to a Stop-WebSite cmdlet, but it still works for all the web sites.

If you have sites that normally not run, you have to exclude them in the second command, like:

Where {$_.Name -ne "Offline" -and $_.Name -ne "foobar.com"}

If you don't have the PowerShell cmdlets for IIS installed, you can use appcmd.exe to do the same, I haven't used that in years though.