I had to recover a ConfigMgr Primary site today where IIS seemed completely b0rked.
The engineer had changed IIS 7's applicationhost.config by hand in the RequestFiltering section, no big deal there, but for some reason all web services for ConfigMgr died after they saved the file.
On the surface it looked broken. IIS would start OK, but there were a stack of WAS errors (Windows Authentication ...) being generated and none of the ConfigMgr web-based roles responded.
I returned the previous IIS config using the %WINDIR%\INETPUB\HISTORY contents (google it) and still no joy.
The long and the short of it, nothing was broken, the application pools had simple stopped and needed to be restarted.
They should look like this:
Once started, the show was back on.