Well, in order to avoid
"monster of the week", how about a previously unknown civilization that lives on the continent.
Something like a primitive culture/civilization of either Nenanderthals (my first choice due to their hardiness) or primitive modern man. 50,000 to 100,000 years ago, a group of these people set out from South Africa or the southern tip of South America (during the summer of course). - I'm not sure of their motivation though. - They find themselves trapped in ice as winter approaches and have to head further south (inland) in order to find shelter. They find a tunnel through the ice (created by a volcanic fumarole) that leads them underneath the ice sheet. Underneath the ice sheet, and also underground in complex cave networks (think the Underdark), they find an alien but thriving ecosystem: underground and under-ice lakes warmed by geothermal/volcanic heat, full of strange fish and creatures; a thriving moss/lichen vegetation flora, some that even glow and provide light; and possibly, animal life which has become extinct throughout the rest of the world - rare marsupials and maybe even anklysaurs (would make great beasts of burden for this culture).
Going with the Cthulu feel, have the civilization be a little more like Morlocks. Also perhaps under the control of some "Elder God" (like an Aboleth or something). (Or maybe two civilizations, one primitive but relatively normal, and one Morlock-like subjugated by and venerating an "Elder God".)
Not to suggest the campiness, but the old
"Land of the Lost" series might have the type of feel you're looking for in a long term campaign. Maybe the characters are somehow cut-off from returning to modern civilization and they must learn to survive in this strange world while trying to find a way back home.
Another idea, kind of going the
"AVP" route, there are ruins of a much older
Cthulu/Alien-esque civilization buried under the ice or underground in the Mountains. Possibly inhabited by primitive humans, possibly inhabited by modern but alien humans, or just inhabited by aliens themselves.
Just remember, Antarctica is bigger than both Australia and Europe. That's a lot of real estate, with 97% buried under ice. There could be an entire civilization under the ice, or in cave networks in the underground/mountains, that could survive undetected for centuries. Also, with Antarctica once connected to Africa and Australia while a part of the super continent Gondwana. It once had a flourishing ecology with temperate forrests dominated by ferns and dinosaurs, and then now-extinct marsupials while still connected to Australia. Anything from that past should be fair game.
Anyways, just some ideas to knock around that may help you get the ball rolling.
