Mission tree

I don't think nobody ever made one, I encourage you to replay the game and make it for everyone ! ;) It should be pretty simple, given the very small number of missions and few variants.
I can recommend some programs for creating the trees...I used a demo version of Edraw Max to do the Standoff trees.
Other people also mentioned Visio which comes with MS Office. You may want to look at it as well. I was going to try it out for the Ep5 mission trees.
Visio integrates with the rest of the MS Office programs, but it is not a part of any Office 2007 package. It's about as pricey as Office itself, but it does work very well for this sort of thing.