Sure

I take the same flat rate deposit from all new clients - $XXX regardless of what they're contracting for or how many hours they expect to use each week. No calculations, just the same amount across the board. That's paid back to the client on an invoice after six months of paying on time. I have numerous clients who are no longer on deposit - they've long since surpassed the six month mark.
I do charge a late payment penalty on invoices not paid at 15 days and again at 30 - regardless of deposits on record or not.
As to large projects, if the same client wants a website, for example, I request another flar rate deposit against the project itself - depending on the scope of the project the deposit can be anywhere from $500 to $3,000+