Well, my favorite reference would have to be much of the score. Quite often, it very much kept alive the feeling that I was indeed watching something with its roots firmly planted in the scope and atmosphere of a TOS episode.
Not necessarily my favorite, but I don't think I've mentioned before that I liked seeing the admirals on the academy council with references to the original series, such as Barnett and Chandra.
The uncertainty of the warp speeds. The trip to Vulcan seemed amazingly short. It seemed like it took just minutes. I think Sulu says to Pike that theyve reached "maximum warp" and from there its just a hop, skip and jump. Now maybe theres some story time thats supposed to be in there somewhere, but it sure seemed like a quick trip. Later, after the events at Vulcan, Spock orders the ship to the Laurentian system at Warp 3. Now, maybe the Warp power was down from damage, but that seemed a slow speed under the circumstances. But thats like TOS. Kirk would say "Warp Factor 1" or 2 when that wouldnt make alot of sense unless they planned to take a long long time to get to their destination.
There was another thread, somewhere on this, was it in the TOS forum? I can't find it off hand, maybe worth doing a search for.
You may be thinking of this one from the TOS forum. There have been at least two or three in this forum, besides, either TOS-specific or about references to any of the other series.