Autoruns is probably the most comprehensive startup analyzer around, but disabling the entries from there would do the trick.
Disabling entries from msconfig, will make the computer not boot in "normal" mode. If he's as picky as (im very very picky) he won't like that.
open regedit.exe and delete the entries manually. example HKLM\SOFTWRE\Microsoft\Windows\CurrentVersion\Run
Autoruns is great, some stuff like MSConfig miss certain keys like the userinit key and the shell keys. Nasty malware likes to use these keys to run stuff on startup when programs monitor the normal startup items.