I ran into an interesting problem this week in SharePoint (MOSS). On some sub-web sites, the attachment (paperclip) icon disappeared. I also noted that some other miscellaneous icons were replaced with the ugly red X. However, this problem did not occur in the top level site in the collection. Odd.
I checked permissions all over the place and couldn't find any reason why this would be happening. Then I discovered through a forum that the application pool settings do indeed affect permissions to virtual directories. A colleague had recently changed the primary application pool for our portal as a troubleshooting step with Microsoft support (we're experiencing some memory leak issues).
The changed application pool propogated down from the web site to the virtual directories, but not to the applications below (such as 'images'). Voila! Changed the app pools on those applications to the new app pool and everything worked again.
Another SharePoint mystery solved!