Have seen a few instances of this lately – on 2003 Server running SP1 or SP2 with WSS 3 or MOSS 2007 installed, if you open up the IIS 6 Control Panel applet from Admin Tools, it takes about 20 seconds to appear and displays nothing except the name of the server you are currently on. There are no other nodes that appear – No Application Pool folder, no Web Sites folder, nothing.
According to this article (http://support.microsoft.com/default.aspx/kb/946517/en-us), it seems that the SharePoint timer service (OWSTimer.exe) can compete for IIS with other processes and cause this situation to occur. A temporary fix can be achieved by running IISRESET on your site (and bringing down your sites momentarily), however if you call MS Support they’ll send you the fix for free.
I’ve only seen this on 32-bit 2003 servers running SP2, but it looks like it affects all 2003 server versions running with a service pack.
Good luck and happy troubleshooting!
PS: As an aside – The MS internal support article indicates that this hotfix is part of SP3 for 2003 server. Huh? I spent half an hour on the phone with Microsoft support (in India over their impressive VoIP system with audio lag) explaining to them that SP3 was not out yet and probably wouldn’t be out for another 12 months or so – hell, SP2 only came out mid 2007 and OS SP’s seem to roll around every couple of years… They finally came around to my way of thinking, and hopefully will change their internal information. It was only when I rang back again asking for SP3 that they finally admitted it didn’t exist yet 🙂