Where do you think you get the best deal?

A friend told me they got a great deal by booking all the parts of their holiday independently but I often find when I look at hotel websites that the daily rate works out more than if I booked through an agent. I know they can get really good deals with the hotels. I've booked myself holidays previously where I have sourced the accomodation - generally self catering - and then made my own flight bookings and saved money but 'm not convinced this is always the best option.

So what do you think is the best way?