USB Drive Anti-Virus Software
Before we start, note that just about any anti-virus software can fit on a USB drive. Most are not more than about 100 MB and you can get at least a 1-gig USB thumb drive for pocket change now. Just being able to put the files on the thumb drive won't cut it in most cases though, unless you just need to move the files onto the computer itself. Theoretically, you might be able to sneak the clean installation files onto an infected computer and then install it. Some malware would only block the installation sites or the download, so it might work. If you would like a list of free anti-virus software for that purpose, then we have them all covered.
As for specific USB anti-virus software, there are two main options for easy use.
The first is the Avast protection system. Avast is a good anti-virus program in general and they also have a special program for USB thumb drives. It protects the drive itself from infection and can carry out scans on the connected computer. The only big problem is that Avast will only work on U3 USB drives, so this will probably exclude a large number of potential users.
If Avast won't work, then you could try AVG. The AVG rescue disc has a special download option that can be put onto a USB thumb drive. By following the basic instructions, the USB thumb drive can be configured to run the rescue program on an infected computer to heal any infections and even rescue a potentially damaged operating system.
SUPERAntiSpyware has a portable scanner. It is apparently incredibly easy to use, since you only have to download the software and move the files. According to that review, it's far from perfect but it is an easy option if you have an active infection.
Unfortunately, these seem to be the main options. A few of the other popular brands have to be installed on a PC before they can operate. Malwarebytes has specifically stated this on their forums, since there have to be some files installed on the main computer. The same appears to be true of Avira AntiVir. Both of these can be made to run off a USB thumb drive, but it takes a lot of work and a lot of access to the infected computer. If you were able to access your system normally, then you probably would not need to mess around with a USB drive.