As we're starting to see greater traffic, I'm finally seeing some longer comment threads on some posts, like this one:
It becomes quickly apparent, IMHO, that we're in need of some visual/interface cues to indicate multiple levels of comment threading/hierarchy.
One of the best interface strengths of Reddit is how tuned they've made their comment sections - it's super easy to see the threads of conversations as they blossom, and it's key to making the comment areas the real community-driving force they should be. On Reddit, most of the best content comes from great comments, and we need to be doing everything possible to promote ease of reading and commenting.
As a separate item (that reminds me!) - we need to establish a "/r/bestof"-equivalent Topic to highlight and curate the best comments that occur on the site, to ensure they catch visibility and are rewarded with Tops and SuperTops - I believe it's a vital and powerful mechanism to drive best-of-class commenting.