EzPcFix is a excellent tool made by Tom (pcuser) over at UBCD4Win for viewing and modifying auto start locations. It is targeted at Malware removal and can be run natively in a PE environment and scan remote profiles.
EzPcFix doesn't scan for viruses, it shows you what programs are being started on the system and lets you manually remove them, therefore it is recommend for use by experienced users only as the program makes no distinction between virus/malware and legitimate programs.
don't let the simple unstyled interface fool you, this program packs a lot of power!