Many viruses and trojans start when the operating system loads and sometimes following removal instructions didn't stop the madness. Or there's software that is very persistent on the computer and killing the process in Task Manager doesn't stop it. Msconfig allows you to specify what processes run at startup, which reduces the time it takes to begin working and the memory used.
In order to determine which processes are legitimate and which need to be killed, I Googled each executable in MSConfig -> Startup and this site kept popping up in my search when the process was legitimate. When the process was malware this site was not part of the listings...a welcome shortcut. You can also use this site directly to research processes. Of course the user should always be ware, and be sure to check multiple sources before deleting system processes. I usually compare my findings to Microsoft's description.
It was enlightening to see how many software developers use background processes to run software you don't use daily. I disabled them and noticed a much better running system. Also disabling certain applications allowed my computers to work more as expected: when multiple users log onto my lab computers I was able to control whether some software loaded or whether they didn't.