Rates, fees, charges .... sounds like my bank :)
But seriously, I would agree with Bret OR charge a flat rate for each page / animation / effect.
What you have to realise is that its your time / effort and (in some instances) money. Charging a flat rate can be very appealing for some people/companies while charging for different effects appeals more to others. An hourly rate is good too but this then has to cover both of the above.
A friend of mine also quotes a flat rate for a project. The project is defined and a spec. put together. From this a cost can be determined along with a timeframe for completion. This works very well for her.
But, if this is for a friend or associate then charge whatever feels comfortable.
I'm a consultant and charge by the hour. This makes it easier for the client as they can then get me to do whatever they like and still pay the same rate no matter what.
HTH,
Ed