Reading a Controller Pak

First you need to setup the Cart Reader Shield's configuration switches like so:

3vhw5

Doublecheck that the voltage switch is set correctly to 3.3V and that the EEP switch is set to enabled(=towards the back). This connects a 1K pull-up resistor between VCC and the controllers data pin(PH4).

Next plug a N64 controller into the controller plug and insert a Controller Pak into the Controller. Then turn the Cart Reader on.
Navigate to Nintendo 64 and then to Controller. You can use http://rawgit.com/bryc/mempak/master/index.html to manage saved Controller Pak data on your PC.