One of the first program you will need fix a maleware problem.

http://www.malwarebytes.org/

CWShredder cleans out cool websearch and if you happen to get hit by this then using this software should help clean it out. (Click Here for Software)

Some viruses will check your proxy server which will disable your internet to fix this go to : 

Tools> > Internet Options> Connections (tab)> Lan Settings (button at bottom of connection tab) > Proxy server (uncheck)

 

 

Note : Doesnt work with vista or windows 7

Combofix is a freeware (a legitimate spyware remover created by sUBs), Combofix was designed to scan a computer for known malware, spyware (SurfSideKick, QooLogic, and Look2Me as well as any other combination of the mentioned spyware applications) and remove them.

ComboFix allows the manual removal of spyware infections . It 's a specialized effective cleaning tool, which is useful compared to other malware and spyware removers.

After Combofix finished,a report will be created. You can use this report to search and remove infections which are not automatically removed.

 

Combofix Website (Click Here)

A program from trendmicro that shows whats going on with your pc. You should know a little bit about what should and shouldnt be running before using this program (click here)

This used to be the only program I would use. Sadly along the way virus makers seemed to haved figured this out and it has become the second program I goto. One of the tools I use is in advance mode that shows bho's and an advanced startup view. (click here)

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 Me and XP. (Click Here)