SquareCal

This is a tool you can use to check if your Y axis is perpendicular to the X axis.

Some people, myself included, have printed out http://www.thingiverse.com/thing:11978 and noticed that the cable chain arcs to one side. Investigating the problem I have discovered that my Thing-O-Matic's Y stage is not perpendicular to the X axis. This may be the cause of the arcing problem.