I checked around for what others are charging in this area and the independent shops with a flat rate go from $75 - $150 for antivirus/spyware cleanup while the hourly rate guys range from $60 to $100 an hour. I don't think I need to undercut anybody so I'm thinking $100 flat rate for a clean-up job and $60/hr for other types of work.
An extra thanks to Andrew for the list of software needed.