Check for specific stuff

• Check if there are any obvious startup processes that are bogging things down (autoruns, StartupRun, msconfig)
• Check browser hooks — BHO
• Check for suspicious network activity (TCPview, Wireshark)
• Check for rootkits (rootkitrevealer)

General scans

• general spyware checkers
• antivirus blah blah blah

Check for obvious vulnerabilities that could cause future problems

• list all open shares (ShareEnum)
• list listening sockets (TcpView)