Short, non-technical answer - mean sea level. That's not entirely true, and the actual answer is far longer and more technical than you probably care to read, but that's close enough. It's certainly not above the road below, because the GPS knows nothing at all about roads, mountains, or anything else on the earth. Mapping software might, but the GPS doesn't. It just knows the distance to the satellites it's tracking, nothing else.

Maemo Mapper will plot your location, show it on the maps you download, and transfer the tracks to a file if you want. The file can be imported by a number of apps for further massaging.