I recommend using a program such as StartupManger from Kissco
http://www.kissco.com http://www.startupmgr.com/
It monitors changes to the registry that cause programs to be loaded on startup.
As the current prevailing tendancy is for malware to is to write entries into the registry to ensure the nasty gets loaded on startup, if you have some sort of startupmanger running at startup then the chances that some malware will sneak in undetected are greatly reduced.
There are other StartupMangers around but Kissco's is the one I use.