I think you might find GraphViz interesting. It's a pretty easy-to-use program that allows you to produce graphs from a text file. You can add labels, color, edge weights, etc. All you'd have to do is write a text file "linking" the reactions. You can even name the nodes of the graph in an intuitive manner. Here would be an example:

digraph {
NaCl [label = "table salt"];
Na -> NaCl;
Cl -> NaCl;
}

And then GraphViz turns that into a picture. Specifically, you'll be intrested in the program called "dot" that comes with the GraphViz package.

Hope this helps!

-- Dylan