I've been making a visual decision tree (flowchart) and I've more or less finished Rin and Hanako. I do plan on finishing this.
I realize that it is a bit hard to understand, but the general idea is to move downwards. Boxes with titles (without numbers) are events. Boxes with numbers are choices and are numbered for convenience. Solid lines indicate which scenes connect to which and dotted lines show requirements for specific scenes. Forks are either caused by choices (in which the next boxes are numbered and all connect to the previous box) or by events which require a specific number of flags (in which the next boxes are NOT numbered).
The best way to use this flowchart is to pretend it's a subway or bus map. You know your originating point and your desired end point, so just trace the route that goes there, keeping the notations (such as flags) in mind. There's further help in the image file if you need it.
View it here: http://i.imgur.com/t58gW.png
I do think some things (such as where flags are earned) are wrong, so all corrections are encouraged - but after I finish the game myself!
EDIT: added how to read the flowchart
EDIT 2: Updated flowchart for Shizune's route. Note that a lot of the flags are noted by SC - this is just in case people want Misha's scene.
EDIT 3: Here (http://filesmelt.com/dl/KatawaShoujoFlowchartv20.png
) is a brilliant flowchart made by Feuver - it's much easier to understand and, at this point, more complete. I'll still be updating and posting mine just because I like completion.
EDIT 4: Uploaded the full Emi route. I'll now finish off Lilly, upload that, and then release the full flowchart with every scene in the game. I've also removed the embedded picture because that was annoying to scroll through and it wasn't readable anyways. Also, apologies for the mess around the top of Emi's route - I might fix that if I feel ambitious (alternatively, just stick with Feuver).
EDIT 5: Uploaded full Lily route and fixed SOME (but not all of) Rin's route. I'm kind of drained from the entire experience of Lilly's route, so I'll get around to tying up loose ends and adding the final scene in Rin's route later than usual.
EDIT 6: Uploaded the COMPLETE flowchart. Every scene and every choice is now there. Of course, there is a bit of a clusterf*ck around Emi's route because it was so far from Don't Panic and the Student Council's (Shizune's) route. I might (emphasis on might) fix the random arrows going everywhere, but I may be too lazy too. It's been fun.