Despite not being a popular story I think I would go with The Web Planet. I think half of the problem with that is that it looks so poorly made. The story really isn't bad, it just looks it. And the noises are frustrating too. With an overhaul I think it's popularity could really grow.
I agree. I saw The Web Planet as a kid when it was originally on and it blew me away - it was actually one of the stories that stuck most clearly in my memory from that period. It does suffer now from the limited effects quality when it was possibly the most amibitious story up to that point, but I think it's a fine story.