Most startup monitors monitor a few registry keys on top of some folders
&files (eg wininit, autoexec.bat). In theory, you should be looking at
startup monitors that handle both files and registry, but in practice, the
later is far more important because there are literally dozens of ways
malware can autostart via the registry as compared to via files.
Here's a interesting post comparing some of them. Includes freeware like
teatimer, Winpatrol and SSM (not really freeware since it is time limited).
http://www.wilderssecurity.com/showthread.php?t=32823
Others not on the list that monitor registry keys include Mikelin's startup
monitor, regprot (very very limited).
I just use the Tea Timer function of Spybot S&D. It'll tell you everytime
something tries to change a startup or services registry entry.
MJ registry watcher is a heavy duty freeware registry watcher that seems to
be developing quickly.
http://www.jacobsm.com/#downloads
You could also get utilities like autorun, starter,startupcop, autostart
viewer etc, but these don't actively monitor.