Wow. Lots of good things here.
I never considered the influence on DND in those terms before, re: Plane Sailing, and how Conan, et al, ended up leading armies. Happened in Amber as well, which I think is listed as an influence in the 1E DMG. Very interesting. Thanks!
To the OP, I think there are a LOT of things like starship combat in 3.x.
Mounted Combat (Feats) - As others have said. However, I am going to make it more generic and say Feats in general. While some have use most of the time, any of them could be too specific in the right situations. For example, creation feats are no good if the campaign doesn't allow the time/gold/xp for them. The chain to Whirlwind attack is no good if lots of foes aren't attacking, etc.
Certain spells - This is tough. Some spells are useful but still meant for mass combat, like Meteor Swarm. Death Spell is the same. Cloudkill always sounds neat but an equal CR won't be much effected. etc. I am not arguing that they are still effective. I just know that when I was playing DND, I grabbed any and every spell I could but always ended up using the same twelve spells over and over.
Prestige Classes - The idea of them, as I understand it, was to fill a specific niche. So, already they are specific in *some* way. I think the really good ones are the ones that are specific in ways that allows them to be useful in more situations. So, Loremaster is a good specific one that allows use in potentially many areas. But I am sure there are others that aren't, and I am no expert on them. In general, though, I am sure that if the campaign went in a different direction from the prestige class, it won't be as helpful.
DR - 3.5 seemed to go the way of starship combat. When it was a nice, simple #/+# it was generic. When it went to bludgeon, silver, magic, good, etc., it seemed to make it like the fighter had to carry a dozen different types of weapons, of different plusses and materials, to be effective. Don't get me wrong. I liked some of the specifics, like silver for lycanthropes and bludgeoning for skeletons to name a few, but think they should have had a "plussed" equivalent as well.
Magic Items - I think the magic item compendium talked about the "big six" categories that are always useful. So, assumably before then, anything that wasn't in the "big six" would be niche. Decanter of endless water, ring/helm/gauntlets of swimming, vest of escape, and I am sure there are more.
I personally am excited about the Saga rules. This is something that might bring me back to using d20. I am of the opinion that d20 is still too rooted in wargaming and I want my games to be about the heroes, not the armies. That's me and my style, though, and that's not for everyone. But making the game more about the individuals is a good thing, imo.
Take care.
edg