I've always used SysInternals AutoRuns, since it has more then just the RUN registry entries, and includes stuff like winlogon notify hooks and so forth.
It's funny, how people just ignore the dialog that appears after rebooting with msconfig enabled, which clearly states that it is more a diagnostic tool then anything.
I've never really liked the tools that include a method to "disable" and "enable" them, by moving the particular keys into and out of a subkey of the run key.
Why? Well- you never really know what MS might do in the future! maybe they will change it so that values in subkeys are run in the same process address space- meaning these "disabled" items will all run anyway.
I've always opted for deletion.