McAfee Avert Stinger is a stand-alone portable antivirus tool which can detect and remove some malware.
At its simplest, all you have to do is download the program, launch it, click Scan Now and wait to see what happens. Stinger's straightforward on-demand scanning shouldn't conflict with any other security software, so you can run it alongside your existing antivirus package without any problems. And if the program detects any threats then it'll remove them for you.
Stinger does have a few interesting settings hidden behind the Preferences button. You might want to check the "Boot sectors" box to ensure the program checks for boot sector viruses, for instance. And if you're sure your system is infected, but Stinger can't find anything, then you might try increasing the heuristic sensitivity level. This makes it more likely that the program will spot suspect files, but also increases the chance that it'll highlight entirely innocent programs, so you should also change the "On virus detection" option from "Repair" to "Report only", at least initially.
Please note, Stinger only detects the most common malware specimens (click the List Viruses button to see them all), and offers no real-time protection measures at all, so it's no substitute for a full antivirus package. The program can be useful, though, if you've been infected by a virus which your regular package has missed: Stinger just might be able to find and remove it for you.
Note this is the 64-bit version of Stinger.
Stinger is limited in the malware it can detect, but as it's also portable, free and unusually configurable, the program still earns a thumbs up from us.