On a Windows Server 2003 SP2 Standard Edition with IIS 6.0 and only one site running - we have strange issue.
There are multiple instances of w3wp.exe process running, i.e. about few hundreds.
When you try to open Task Manager, few tabs can be missing and it really looks weird:
It works fine after reboot for some time, but then the issue appears again.
Oddness in GUI elements generally has to do with resource exhaustion issues. What that many running processes I wouldn't be surprised if you've had some kind of resource leak.
I'd get Performance Monitor running and capture data to feed to the Performance Analysis of Logs (PAL) tool. This tool does a great job of identifying leaks. Getting started with PAL isn't too bad-- read over the documentation and I think you'll get going fairly quickly. You'll be using operating systems' built-in Performance Monitor to log a set of performance counters to files, followed-up by the PAL tool (which you can, and should, run on another machine) to analyze the log files.
The "System Overview" report in PAL will tell you what you need. You'll need to log the following counters to give it the information it needs:
