This plugin allows a user to choose which matrix combinations he wants to run, as opposed to the default behaviour where jenkins runs all combinations and translate it into a groovy condition such as:
axis1=="axis1value1" && axis2=="axis2value1" || axis1=="axis1value2" && axis2=="axis2value2" || ...
After installation a new type of parameter was added (Matrix Combinations Parameter). 
- Configure your matrix job and add exactly one parameter with this type
- Fill the name of the parameter
- Define the Axes as usual
After clicking the build, the user gets a html table with a checkbox for each matrix combination.
After clicking the submit button, only checked combinations will run.
Many thanks to Nathan Grunzweig for giving me the idea and help with the implementation of this plugin.
I would also like to thank Christian Wolfgang, who developed the Matrix Reloaded Plugin which gave me the inspiration to implement it.