Based on my personal preference, experience and habit, here is what I use.

Backing to line: nail knot
Line (without loop) to 1 foot butt section: nail knot
Butt section to leader: blood knot
Line (with loop) to leader: Perfection loop to line loop
Leader to tippet: Surgeon's knot
Tippet to fly: improved or unimproved clinch or non-slip loop. It might just be me, but in flourocarbon, I have been having better luck with the unimproved clinch. I use the loop for streamers.

I use several different loops. The perfection loop is quick an easy but not so strong. I use it for the butt end of leader, since it's not the weakest point. When I tie a fly to the loop I use the non-slip mono loop. When I want a strong loop, I use a figure-8 loop or a king sling.