This is an utterly predictable problem.
News.YC has been mentioned in enough places -- like Reddit, where I migrated from -- that it's been gathering some influence from those places. PG has been curiously adamant about not doing anything algorithmically to address this, instead insisting that somehow this forum will just never accumulate the kind of cruft that every other web-based forum accumulates.
I think that web-based forums have to follow one of the basic rules of capitalism, in that it has one of three states: either it's dying, or it's growing slowly, or it's growing quickly.
Interesting conversations and submissions happen as a way for people to signal information to other people that they think might not be aware of it, and might find it interesting. Assuming it were possible for a forum to never either lose nor gain participants, eventually the participants would share most of the information that they weren't mutually familiar with, and those that were interested in external sources of information that they weren't initially aware of would begin to follow them, and there'd be nothing left to share. The forum gradually gets quieter, and dies.
Or, the forum can grow. It may grow quickly, as with Reddit or Digg or Fark or what-have-you, in which case it has a natural tendency towards more mainstream topics. Or, it can grow slowly, like News.YC, but it still gathers a little bit of new blood, and inevitably, that new blood brings a certain fraction of mainstream interest along with it.
The funny thing is, a forum in a slow state of growth will tend to accelerate into a faster state of growth, as the gradual increase in mainstream topics draws the interest of a larger cross-section of people.
So, the trick is to enforce a slower state of growth without killing it altogether, and I haven't seen any willingness here to do that.