"Autoruns": This utility, which has the most comprehensive knowledge of auto-starting locations of any startup monitor, shows you what programs are configured to run during system bootup or login, and shows you the entries in the order Windows processes them. These programs include ones in your startup folder, Run, RunOnce, and other Registry keys. You can configure Autoruns to show other locations, including Explorer shell extensions, toolbars, browser helper objects, Winlogon notifications, auto-start services, and much more. Autoruns goes way beyond the MSConfig utility bundled with Windows 98, Me and XP.
Those two software are free and very good, they give clear understanding info on those files. you can Download them at my download page.
This might be a little difficult for some people to understand and use, but just install them and see what is running in your computer, you will be amaze of the amount of files and process running in the background of your computer.
But don't worry, if you follow my step by step instruction on How to remove trojan virus this will get clean automatically.
4:=Assuming that the scan is finish and that you remove unwanted process and start up files, now let boot up in normal windows and continue on with a online scan.
Now i always use a online scan sometime two to make sure everything is clean.
I like to use Free online scanner
it seem to work only with IE and not Firefox. Go to the bottom right of the page an click on "Free Online Scan"
Press the agree button and accept and install the activeX control, it is needed.
Then it will start updating itself and load to your computer, and let it scan the complete process.