Autoruns, from SysInternals (recently acquired by Microsoft), is indispensable when removing malware manually.

Autoruns is a standalone utility that does not need to be installed on your system.

It can be simply downloaded, unzipped and run (link below).

Use Autoruns to Manually Clean an Infected PC

This makes is ideally suited for adding to your portable utility collection on your flash drive.

Most of the entries presented in Autoruns are legitimate programs, even if their names are unfamiliar to you.

Keep in mind that some malware is harder to remove than others.

Autoruns window

Sometimes the instant that you remove the Autorun entry, the malware that is running replaces the entry.

ar_entries

Suspicious entries in System32 folder

Suspicious entries in Registry