According to Cook's Illustrated/America's Test Kitchen the cone brewing system made popular by Melita is the best way to brew...for now. Okay so what's the best way to do it?
The key, they say, is for your coffee to be done brewing in 4-6 mins and using something like 180 deg F water. Now I neither time my brewing or test my water for temperature, but I have found that if I make coffee in my 2 cup cone filter in the following way I get a great cup.
My favourite mugs are 1.5 cup mugs. Don't know why, just happens to be so. So I heat 1 2/3 cups of water up in the microwave. Regardless of what you think of microwave energy, this is an energy efficient way to heat the water. My microwave takes about 4 mins to get the water to the right temperature.
So while the water is heating I either scoop two scoopers (the little conical coffee measures) of ground coffee or two scoops of beans. Grind, if needed, other wise I put the coffee into a #2 unbleached coffee filter in my little 2c holder. I like unbleached filters for environmental reasons, not only am I not supporting the use of chlorine in the bleaching process, I compost the filter and ground and don't want it in my garden, thank you. That being said Thrifty Foods sells cone filters bleached with ozone (O3) or hydrogen peroxide (H2O2). These are fine and used a whole pack and didn't notice any odd flavours in my coffee.
Okay once the water is hot I pour enough to cover all the grounds well then stop. I let this drain through and site for about another minute. This gives the grounds a chance to moisten and expand. Coffee grounds are hydro-phobic (repel water), so this step helps the brewing process tremendously.
Once the grounds are good and wet, I pour in the rest of the water, slowly. If I'm careful and go relatively slowly I can get the rest of the water in this way without a pause. Then I wait, and often forget, for it to finish. When all the water has perked through you're done. Now, this is all going into the mug I'm going to drink out of, so if you're brewing into a larger vessel, you'll have to pour in stages or the cone will overflow (bad, and messy).
I'm a stickler for the proper water to coffee ratio, so if I had a larger cone and vessel I'd either still heat the water in the microwave or heat it in a tea kettle and pour into a measuring cup (this would also cool the boiling water a bit so you don't overbrew your coffee making a bitter cup).
Hope this helps you make a great up o' Joe!