Security Update 2006-003 (#3): More on startup woes -- check the other StartupItems folder; Active Directory issues; more
Security Update 2006-003 (#4): StartupItems removal fix for startup issues confirmed; Removing the update; Other freezes; more
One problem that may occur when logging in to OS X is an error warning that mentions insecure startup items.
A few users who have installed Snow Leopard on their systems have run into a problem where upon logging in the system claims the "Startup Items" folder is insecure and items from this folder will not be used.
Repairing drag and drop in Mac OS X 10.2.8
Apple echoes previously published QuickTime 7.1 startup workaround in Knowledge Base article
Troubleshooting QuickTime 6.3: Conflict with DuoConfigurationService
Security Update 2006-003 Special Report: Startup stalls/freezes after updating -- fixes
If you are experiencing problems with a menu extra and can't seem to remove it by standard means, it may have a nonstandard implementation, which will take a couple of steps to root out and uninstall.
Mac OS X 10.4: M-Audio device issues, workarounds