I know that cave paintings have been found in many areas around the world, suggesting that prehistoric people would have explored them to some extent, but are there any locations where evidence of exploration has been found particularly far from the surface / entrance?
According to the Nov 29-Dec 5 2014 New Scientist (p. 40) there was a bonanza cache of early hominid fossils found in a very difficult to access cave 30 meters underground. The Rising Star caves are in South Africa 30 kilometers north-west of Johannesburg. The cave itself is only accessible through an 18 centimeter wide crack past a narrow formation with 15 meter drops on either side. They found many, many bones. More than just a few individuals it sounds like.
It looks like Lee Berger is the paleoanthropologist more or less in charge, even though it was cavers who made the actual discovery - he's the one who recognized it for what it is.
There's a large team working on the excavation but they won't be announcing results of a big workshop until early next year.
Native Americans ventured deep into Mammoth Cave in the central US. The cave is actually a good environment for preservation, so many artifacts have been found.
Thousands of artifacts including gourd bowls, mussel shells, cord, pottery, woven cloth – even a handful of petroglyphs – attest to millenia of aboriginal exploration. From 4,000 years ago until nearly 2,000 years ago, this Native American culture explored and mined the upper three levels of Mammoth Cave for a distance of over six miles, seeking gypsum, selenite, mirabilite, epsomite, and other related minerals. http://www.nps.gov/maca/historyculture/history1.htm