ITT: Indiefag bawwwwww.
No but really, Cave Story is probably the second most well-known freeware game (behind Dorfortress of course). Indie gaming, much less freeware indie gaming, is a small market compared to the mainstream high-budget FPS machine, so you're not going to find a lot of people who have heard of it.
The reason indie games are indie is because most people can't be assed to care about the industry that much and go looking for lesser-known titles that are made to appeal to more... devoted gamers. Taking an interest in Call of Duty and not, say, Trine, isn't a bad thing, because not everyone is that into games. I'm guessing lots people reading this don't read many lesser-known books or watch independent films.
And yes, immortalshippo, all your words are invalid, so maybe stop using them.