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The software I use is Quantum GIS or QGIS for short. This is open source and is free.

I have used Google Earth, Garmin Base Camp, Compass and Therion for producing the input data for QGIS.

I use Therion for producing surveys and one of the export options is an ESRI format. This is a GIS shape file which is basically a small database which defines the geographical information of the object. The object may be a survey, a cave or a whole cave system or even all the caves in a specific area.

To export an ESRI shape file from Therion there are two options, 2d Map or 3d Model

These are imported into QGIS as a vector layer. Here are examples of the layers produced for a single cave.

QGIS Layers