Malicious software is running at epidemic proportions nowadays so it's essential that a set of tools for effectively removing them be available. Since no scanner is able to pickup and remove 100% of malicious software out there, it's imperative that there be more than one tool to do the job.
Here's a list of five essential scanners for removing malicious software:
Malicious software removal tool - Microsoft's own targeted removal tool. It's not a full blown antivirus solution but it's very effective against viruses on its list. It also does not require installation which makes this a portable tool ready for your USB flash drive.
Malwarebytes' Antimalware - This free tool detects and removes adware, spyware, trojans and even some rootkits. Just install, update and run a quick scan. There's a full scan that takes a long time to complete depending on how much you have on your hard disk but I find you rarely need it. The quick scan works wonders in most cases and it's much faster to boot.
Kaspersky AVPTool - A daily updated tool that installs itself on launch and gives the option of uninstalling itself on exit. AVPTool can be considered as a heavy duty "targeted" scanner only it's a full fledged Kaspersky antivirus engine and database. The downside is AVPTool is rather large for a portable scanner and needs to be downloaded daily to maximise effectiveness. There's no visible update function although it does warn you if it thinks the version you're using is too old.
Bitdefender online scanner - Browser-based Bitdefender antivirus scanner. The only downside to online scanners is that it needs to run from Internet Explorer. Since there's tonnes of malware that hijacks Internet Explorer, this is often something you'll want to run after you've removed as many malicious software as you possibly can using other offline tools. As a bonus, there's also a free Linux version of Bitdefender that you can install and run from a Linux USB bootdisk.
Eset online scanner - Same as Bitdefender online scanner. Run this after running other offline tools.
Spybot Search and Destroy - Spybot S&D hasn't been in the limelight for a while but that doesn't make it any less effective. It's specially designed for adware/spyware removal and is usually very effective at it, too. The other tools may miss out some malware they consider less "dangerous" or "critical" so use this to clean them up.
How to remove malware from Windows
Bitdefender on Ubuntu
F-Prot on Ubuntu LiveUSB