As time goes on, we are doing more and more work with advertising agencies. For those of you who are working with agencies (and even direct with clients), are you charging a deposit? Half upfront? Mile-marker payments?

If I'm not doing hourly I ALWAY charge a deposit.

Depending on the job it's usually 1/3 or 1/2. Once a client locks in a time it affects what I can and can't book for some future period even before the job starts.

Yes, charge a deposit - non-refundable. Or maybe to call it a pay as you go and charge in advance for various parts of the project.