The three that are obtainable in game and are also save-able would be Trojan's Roar, Wings of Behemoth, and Elemental Stone.
Trojan's Roar: Beat game on Impossible mode (not sure what first version was, but all recent ones that you would most likely play would have it).
Wings of Behemoth: Beat game on Nightmare mode (same as TR).
Elemental Stone: Kill Eternia, which spawns on wave 10 of endless waves, which also needs Nightmare, air, and invis to spawn and get stone (she does still spawn on lower difficulties with air/invis, you just don't get stone). In addition to that, you need to either have 301 kills, 60k produce/lumber, or get the killing blow (which is pretty unreliable outside of solo). I know this was introduced in 6.40, but had a bug where only killing blow got the stone. Your best bet is probably 6.42.
Some others that are worth mentioning are Slujj Hat and Silvering, which were obtained from forum events. They still are obtainable, but only through the starter package under donate tab, which also gives a tiny lv 1 lumber mill; anything past lv 1 is only available to a few people.
Otherwise, items like Horn of Voortr'hal, Fan Art Scrolls (might be a flower now I don't know), and the like aren't obtainable in just about any way now, and only a select few people have them.