I just finished helping a friend remove some pretty bad spyware from his system. In addition to the usual removal tools – AdAware, and Spybot I found the Autoruns utility from Sysinternals to be very useful.
It is a comprehensive piece of software that will allow you to see every possible startup program in one place. It beats searching through the registry by hand.
Best of all it is totally free, and can be downloaded from Microsoft here:
http://download.sysinternals.com/Files/Autoruns.zip
More info about the utility can be found here:
http://www.microsoft.com/technet/sysinternals/ProcessesAndThreads/Autoruns.mspx
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