WinPatrol Plus is a very handy program, since it covers such a wide range of placements, more thoroughly than other startup programs.
e.g. Today I helped a friend to read his BHO page (IE Helpers). Similar stuff for the Windows Scheduler, Active X, etc. all in one place, easy read. The great strength of WPP is this security aspect. As a startup program controller, there are more elegant, as a security overview of startup, WinPatrolPlus is really kewl.
For warnings, the Plus is far more real-time than the polling of the non-Plus, so if you are going to have the program, Plus is proper. (Plus the support for BillP.)
I am not sure how extensively the warnings are triggered, since the only issue is startup. Right now I get warnings from these programs, WinPatrolPlus, AnVir Task Manager (when I have it loaded), Avira anti-virus, Online Armor, and Zemana. On a warning level AnVir is surprisingly robust, Avira is not popping up much since it is simply virus oriented and I handle email on my own, Online Armor is the mainstay, Zemana is an auxiliary trial emphasizing keylogger, screenread, etc with a neat log. And WinPatrolPlus (Scotty) which I probably should note closer how it works.