Below is a list of the most popular/useful free anti-spyware programs that, when used in combination can help clean your computer from most current trojans:

My favorite anti-spyware tools, updated 2017
Malwarebytes' Anti-Malware - great free version of anti-malware. Just make sure to stop any memory-resident always-on features.
ADWCleaner - cleans unwanted browser extensions and hijacks in most common browsers (Chrome, IE, Firefox,etc.)
CCleaner - remove unused/old/corrupt Registry entries, temporary files, clear internet history, etc. in a couple of clicks.

Other anti-malware programs:
SuperAntiSpyware - great anti-spyware tool
Spybot S&D - one of the better anti-spyware tools
Lavasoft Ad-Aware Free - another solid anti-spyware program
Hijack This - lets user scan/fix key areas of the Registry and hard disk, helpful against browser hijacking, deleting malicious services that start with Windows
SDFix - removes some persistent rootkits and dlls that can't be deleted with the above tools, run in safe mode

Check Suspicious Files
Some virii and trojans are detected by only a few tools, if you're suspicious of a file you may want to run it through this great online tool, which checks it with over 20 leading antivirus programs:
You'd be surprised at the number of malicious files detected by less than 25% of all major security programs.

MS Antivirus tools/scan
Microsoft Security Essentials - free Microsoft antivirus software
MS Windows Live Safety Scanner - (click full service scan) can be used in addition to your local antivirus software