The version of Android originally on the device as supplied by the manufacturer or phone network, including any customizations, alternative interfaces and updates.
Stock Android can be thought of as the software that was loaded on the phone while it was sealed in a box in a phone shop's stock room, or what would be installed if you sent it back to the shop/manufacturer for servicing, or official updates.
Various manufacturers have their own custom interfaces and collections of modified apps that they install on the majority of their devices as part of that device's stock OS, these include HTC's Sense, Samsung's TouchWiz, Motorola's MotoBlur and Sony Ericsson's Timescape and Rachael interfaces.
For a "Pure Google Experience" phone such as one of the Google Nexus devices, stock Android will be just the plain, vanilla Android OS.
If you have rooted your phone or installed a custom ROM then you no longer have a stock version of Android on your phone.