ALL, though I didn't select the swift tracker simply because we tend to ignore the RAW DCs for skill checks in the first place - or at least stretch the rules. Like we allow anyone to move at full speed while stealth/move silently/hide. Or forget the modifiers in a lot of cases (bluff checks?) so, something that removes a -5 that we don't often apply in the first place doesn't come up too often. So, in MY games it doesn't really apply - thus unchecked. That said, in games where they do use the DCs as written - then it is a good ability and does come up often (I like rangers).
I've played races with low-light vision simply because they have it. Not often, but it has happened. I often play elves so it is a frequent thing to come up.
Stoncunning has come up, but it isn't one I like so I tend to avoid it when possible. But in most games I've been in or run there is a standard practice of having the dwarf walk around the exterior wall "looking for doors" aka getting his free check when passing in 10 feet. I dislike the rule but it does still come up. So "it has seen use" in my game, unfortunately.
Timeless body comes up in practically every game where we are playing at near-epic. Frequently when playing monks before that level. Abilities like that one are part of the reason why I enjoy monks - even though they are objectively kind of terrible, they're my favourite class.
Slow Fall is another one of those abilities - and why I get so upset when these types of abilities are removed to make the monk "more fighter" instead of "more utility/rogue." But I have once fallen from the stratosphere and managed to stick the landing by aiming for a tree and slow falling my way down it. Honestly I just wish the slow fall ability reduced the fall damage by Xd6, and eventually turned it into "any height" and ignored the wall requirement.
By "Auras" I assume you mean like the cleric and paladin auras? This is one I never really understood until fairly recently (like 2011

). Now it absolutely is how it is run in my games or games I'm in to explain how 'detect evil' works. Heck last Saturday I explained that as a 15th level evil character I would only have a moderate aura of evil and that was only because we were 15th level. Whereas an 11th level cleric would have a overwhelming one. Helped the party paladin NOT smite me upon first meeting me - got him to rewrite his code

Just on the explanation of the aura.
All of the druid (or ranger) abilities have come up [again see swift tracker] often enough. Trackless step made an antagonist we were chasing once much more annoying - a simple class ability turned a regular encounter into a mini-boss. Woodland stride is also helpful, if niche, in all kinds of maps - especially those that have an 'official' map from some product or other. When actual hazards show up, it is amazing to be the one guy without that problem. The niche part comes in that these kinds of terrain problems don't usually show when the DM is just winging it in a homebrew game (most of the games I play). But it is still a great ability.