There's been a few tool-holders posted, but they never fit my set of tools. So I thought, why not make a modular tool rack that hangs off the side of the Cupcake and that people can customize.
There are two basic pieces -- "lip" and "nolip". The nolip pieces are for lighter objects and fit next the the z-axis parts and rely upon the lip pieces for support. The lip pieces are for heavier parts and clip onto the side of the makerbot.
Due to the space between the z-bolts not being a multiple of the z-bolt mounts, there will be a small gap. If this really, really bothers you, stretch out one of your lip pieces to take up the slack.
These are printed on a well-tuned Cupcake using a Mk6 Stepstruder and the snap dimensions are rather tight. If you have an older extruder, you will probably need to tweak the size of the snap components and possibly the lip.
I've included two "blank" pieces to make it easier to create your own tool inserts.