You will be able to detect and remove a broad range of known and unknown malware even when no UI is available (like safe mode with the command line, for example). Its capabilities make it an outstanding tool to eliminate the most resistant infections. It can also be used to ensure the integrity of the operating system without the risk of conflict with your existing antivirus.
RogueKillerCMD is a quite popular and useful tool for removing stubborn malware. But be warned; you need to know what you’re doing. Malwarebytes is better suited for the home user. While there are a lot of more well-known tools out there that will only scan and delete for you, this tool shows everything it finds. You need to know what to remove and what not to remove, or you run the risk of deleting something you want or need. Your results may vary, but simply put - be careful - do your homework before removing anything or ask someone who is computer savvy like someone in the MajorGeeks support forum.
RogueKillerCMD is typically used by advanced users and techs.
SpywareBlaster helps protect you from known unwanted websites including ActiveX installs, malware, viruses, cookies, and more. Video tutorial available.
Adlice Protect (formerly RogueKiller) is an anti-malware app for advanced users capable of removing stubborn malware based on a list of signatures and heuristic analysis. Command line version available.
Malwarebytes AdwCleaner is a free anti-malware app that deletes adware, PUP's, toolbars, and browser hijackers. Video tutorial available. For complete internet protection, download Malwarebytes here.
Combofix is a freeware application designed for advanced users to scan and manually remove malware and spyware from your computer running Windows XP 32-bit, or Windows Vista, 7 and 8, 32-bit and 64-bit. Video tutorial available. For Windows 10, scanning and live protection consider downloading Malwarebytes.
Dr.WEB CureIt! is an antivirus and anti-spyware scanning tool that will help you quickly scan and cure a computer without installing the Dr.WEB Anti-virus.