What exactly does anti-trojan software do? Is it something to use if you suspect you have a trojan? Or is it something that is running all the time and is supposed to detect trojans as they get into your computer, so that you can catch them before they do anything?

There are three types of trojan programs: free on line scans, SWATIT(free pprogram from the Lockdown Corp) that you use to perform a scan and does not run in real time to prevent/detect a trojan, the paid pprograms that run in real time like a good antivirus program to detect/clean a trojan when it makes its initial appearance. PC Flank has testing and reviews for anti-trojan programs. They also have testing results that show how the various antivirus programs fair at detecting trojans.

There are also specific anti-trojan tools. Many trojans can be detected by AV software, but not removed by it. AV companies then release a downloadable program to remove the specific trojan that was detected by the AV scan. For example, the symantec W32.Blaster.Worm Removal Tool, available for free download.