I think the plumb line / knees over pedal spindle method can give you a good starting point but you still need to experiment some to get the exact spot where you want your saddle to be. I found that I needed to move my saddle back. Not so much for comfort reasons. I discovered that I get better transfer of power from my legs to the pedals if my saddle is back a little. Everyone is built different so you may have to play around some to see what feels right for you.
2004 Colnago Chic - WTB Deva
2008 Blue RC7 - WTB Deva
2009 Colnago Master X-lite - WTB Deva